The San Francisco Bay Regional Water Quality Control Board (Water Board)'s overall mission is to protect the beneficial uses supported by the quality of the San Francisco Bay Region (Region)'s surface water and groundwater. Together, the beneficial uses described in detail in Chapter 2 define the resources, services, and qualities of aquatic ecosystems that are the ultimate goals of protecting and achieving water quality. The objectives presented in Chapter 3 present a framework for determining whether water quality is indeed supporting these beneficial uses. This chapter describes in detail the Water Board's regulatory programs and specific plans of action for meeting water quality objectives and protecting beneficial uses.

The descriptions of specific actions to be taken by local public entities and industries to comply with the policies and objectives of this Water Quality Control Plan (Basin Plan) are intended for the guidance of local officials. The Water Board will consider any proposed alternative actions that are consistent with and achieve the policies and objectives of the Basin Plan.

This chapter describes the watershed management conceptual framework for water quality control in the Region and presents each of the individual regulatory programs that form part of this comprehensive approach. These programs are organized into general categories, including surface water protection and management, groundwater protection and management, wetland protection and management, and emerging program areas. Taken together, these programs constitute an integrated, comprehensive water quality control program that is protective, efficient, and flexible.


In 1995, the Water Board initiated a watershed management approach to regulating water quality, expanding its primary focus from point sources of pollution to include more diffuse sources such as urban and agricultural runoff. A five-year statewide Strategic Plan, initiated in 1995 and last updated in 2001, guides the water resource protection efforts of the State and Regional Water Boards. A key component of the Strategic Plan is the Watershed Management Initiative (WMI), which promotes a watershed management approach for water quality protection as discussed in Chapter 1.

The WMI is designed to integrate various surface water and groundwater regulatory programs while promoting cooperative, collaborative efforts within a watershed that are designed to improve water quality and protect the beneficial uses of the watershed’s water bodies. The WMI is also designed to focus limited funding and resources on the highest priority water quality issues identified by the Water Board in consultation with local stakeholders. The Water Board’s strategy for the WMI is contained in the report titled, “San Francisco Bay Regional Water Quality Control Board Watershed Management Initiative, Integrated Plan Chapter.” This report is a regularly updated planning tool for identifying priorities to be funded by existing resources, as well as priority tasks that are currently not funded. For each update, activities are planned over the next one to two years, and in some cases, over the next five years. The report also contains descriptions of regional and watershed strategies, discusses how the Water Board is structured to implement the WMI, and how the Water Board is implementing a priority-setting process. The WMI builds upon the progress made to date by the Water Board’s efforts, combined with local watershed efforts led by other entities, and it also identifies tasks to be accomplished to fully implement the WMI. Examples of local implementation of the WMI are included in Section 4.1.3 Watershed Management in Countywide Programs and Individual Watersheds.

To implement the WMI in the Region, there are three levels of watershed management: 1) region-wide, 2) countywide, and 3) in sub-watersheds. This watershed management process is flexible and recognizes the existing institutional structures that can implement watershed management to protect water quality.

Some water quality issues are managed at the region-wide level. For example, the Water Board's water quality control program focuses in part on managing the influx of toxic pollutants to the Estuary's aquatic system, described in Section 4.1.2 Toxic Pollutant Management in the San Francisco Estuary System. The goal of this program element is to limit the total amount of pollutants in the entire system to ensure protection of beneficial uses. In cases where evidence suggests beneficial uses are not protected due to specific pollutants in the system, the program described in Section 4.1.1 Water Quality Attainment Strategies Including Total Maximum Daily Loads is initiated.

Other water quality issues are managed at the countywide level. The Region includes portions of nine counties, which all include shoreline on the Bay, permitted discharges to the Bay, and watershed drainage to the Bay. These institutions are therefore well suited to organize and/or participate in a watershed management approach at the countywide level, forming stakeholder groups that include municipalities, other organizations, and members of the public. Examples are discussed in Section 4.1.3 Watershed Management in Countywide Programs and Individual Watersheds. For example, several urban runoff management programs are organized at this countywide level.

Sub-watershed level watershed management occurs within the county-wide framework, as a result of priority setting that is strongly influenced by local input.


The Water Board intends to establish Water Quality Attainment Strategies (WQAS) including Total Maximum Daily Loads (TMDLs) where necessary and appropriate to ensure attainment and maintenance of water quality standards. WQAS and TMDLs for the Region are described in Chapter 7. Section 303(d) of the federal Clean Water Act requires states to identify water bodies that are not attaining water quality standards, and to establish TMDLs for pollutants causing the impairment (non-attainment of water quality standards) of listed water bodies. As such, TMDLs are the pollutant load levels necessary to attain the applicable water quality standards. A complete TMDL refers to the process and elements associated with establishing a TMDL that include, but are not limited to, problem statement, numeric target(s), source analysis, linkage analysis, wasteload and load allocations, implementation plan, and monitoring plan.

WQAS are development and implementation actions associated with implementing (attaining) water quality standards. Complete TMDLs are WQAS, but WQAS are not limited to 303(d)-list pollutants. For example, they may be developed for pollutants for which threat of impairment provides cause for pollution prevention actions and related activities. WQAS may contain, but not necessarily include, all or some of the complete TMDL elements.

The Water Board will establish WQAS including TMDLs at the level (the Estuary, smaller segments within the Estuary, or individual watersheds) deemed most appropriate in terms of effectiveness and efficiency relative to the applicable water quality standard, types and locations of pollutant sources, and type and scale of implementation actions.


The Water Board's water quality programs began decades ago with a focus on controlling the discharge of point sources of pollution such as municipal sewage and industrial wastewater. Since then, highly effective waste treatment systems have been built, essentially eliminating what had been major water quality problems associated with high nutrient and organic loading. In addition, the overall influx of toxic pollutants from point sources has significantly declined as a result of these efforts. Still, certain toxic pollutants remain a great concern.

The focus of efforts to attain water quality goals has expanded accordingly. Further reductions in point source pollutant loadings are being attained through complex, innovative programs often involving numerous public agencies and private organizations. Loading from diffuse sources, such as urban and agricultural runoff, had until recently, continued largely unchecked. These sources are now generally considered to be the largest source of pollutants to aquatic systems. Water Board programs aim to reduce this diffuse pollutant loading. NUMERIC WATER QUALITY OBJECTIVES: WASTELOAD ALLOCATIONS

The numerical objectives presented in Chapter 3 define maximum levels of individual pollutants allowed in the waters of the region. These objectives are based on extensive technical information that relates concentrations of pollutants in water to adverse effects on beneficial uses.

Assuring that pollutant concentrations throughout the whole Estuary system will meet objectives for each pollutant requires (a) information on the fate, transport, and distribution of that pollutant and (b) quantification of loading from all sources, including riverine inputs, urban and agricultural runoff, and point source discharges. When this information is available, the total amount of each pollutant that can enter the system without exceeding water quality objectives can be calculated. The maximum pollutant load can then be allocated among all sources, a process known as wasteload allocation. By considering pollutant influx from all sources, wasteload allocation supports the identification and implementation of the most effective and economically efficient means of achieving water quality objectives in the larger Estuary system.

There are three limitations to this approach. First, there are many pollutants of local concern for which objectives have not been developed and adopted. The objectives for specific toxic pollutants contained in Chapter 3 are reasonable for the purposes of interim regulation because they provide a minimum level of protection in the Estuary; however, additional objectives are necessary to fully implement the wasteload allocation approach. The Water Board will establish water quality objectives for selected pollutants as the necessary technical information becomes available and a framework for assessing economic factors is developed.

Second, the wasteload allocation approach only considers the impact of individual pollutants. Aquatic systems in the region contain mixtures of pollutants in a complex and variable water matrix. Implementation of the toxicity objective described in the following section addresses this issue.

Finally, substances that accumulate in sediment or organisms pose a more complicated problem for water quality control. The additional considerations necessary for these pollutants are described below. TOXIC POLLUTANT ACCUMULATION: MASS-BASED STRATEGIES

Wasteload allocations based on the achievement of numeric water quality objectives will provide appropriate protection of beneficial uses for many toxic pollutants. For some pollutants, however, concentrations in water are not good indicators of their impairment of beneficial uses. Instead, wasteload allocations for such compounds are developed based on mass rather than concentration, and tissue and sediment concentrations. Typically, mass-based allocations require more extensive technical information on the fate and transport of pollutants in the system than those based on water alone.

The Water Board implements the narrative objectives regarding sediment accumulation and bioaccumulation in several ways. These are discussed in greater detail later in this chapter. In general, pollutants are identified and monitored in both discharges and the aquatic system. At a minimum, limits placed on point and nonpoint discharges take pollutant accumulation into consideration. Ultimately, the goal is to develop system-wide, mass-based wasteload allocations for appropriate substances. SCIENTIFIC RESEARCH: ONGOING REFINEMENT OF PROGRAMS

The quantity of pollutants in the Estuary system is the result of many complex and interacting factors beyond the total amount discharged day-to-day. Levels of pollutants in water, sediments, and aquatic organisms are regularly assessed through the Regional Monitoring Program and other surveillance described in Chapter 6.

In addition, implementation of this Water Quality Control Plan involves research and investigation on processes controlling the fate, transport, and distribution of pollutants. In the past, the Water Board has supported research on Delta outflow and associated flushing, sediment movement, chemical transformations within the aquatic system, and biological effects associated with existing and projected pollutant levels.

Information resulting from ongoing scientific research and regular monitoring within the Estuary is continuously incorporated into each of the programs described in detail later in this chapter. In addition, the Water Board typically requires technical investigations in situations where water quality problems have been identified but not enough information is available to craft appropriate courses of action. As a result, programs are constantly evolving as better scientific information becomes available. RIVERINE FLOWS, SYSTEM FLUSHING, AND POLLUTANT LOADING DELTA OUTFLOW

In addition to pollution control measures, achieving water quality objectives and protecting the beneficial uses of the San Francisco Bay Estuary system (particularly fish migration and estuarine habitat) are depends on freshwater outflow from the Delta. Adequate freshwater inflow to the Bay system is necessary to control salinity, to provide mixing (particularly in the entrapment zone), to maintain proper temperature, and to flush out residual pollutants that cannot be eliminated by treatment or nonpoint source management. Except for local drainage and wastewater discharges, Delta outflow provides virtually all the freshwater inflow to San Francisco Bay. However, the availability of adequate Delta outflow to meet these needs is very uncertain because of the existing and potential upstream diversions of water and fluctuations in rainfall.

The State Board first addressed the issue of the Bay's inflow needs in the Water Quality Control Plan for the Sacramento-San Joaquin Delta and Suisun Marsh in the Water Rights Decision 1485, issued in August, 1978. In these documents, the State Board established maximum salinity standards (but no corresponding flow standards for the Delta) and required the two major water diverters to conduct research and determine:

  • Outflow needs in San Francisco Bay, including the ecological benefits of unregulated outflows and salinity gradients established by them; and
  • The need for winter flows for long-term protection of striped bass and other aquatic organisms in the Delta.

In 1993, estuarine scientists and managers associated with the San Francisco Estuary Project recommended development of salinity standards for different parts of the year to be used in conjunction with flow standards. Specifically, they indicate that average upstream positions of the near-bottom 2 0/00 isohaline would be an appropriate index for salinity standards.

Technical evidence developed during the Estuary Project process and the State Board Bay/Delta hearings will be used to help formulate future amendments to the Basin Plan. SAN LUIS DRAIN

The San Luis Drain is a proposed method of funneling agricultural runoff from the San Joaquin Valley into the Delta.

Agricultural irrigation in the San Joaquin Valley leads to high salinity concentrations in the soil, which may be harmful to crops. To alleviate this condition, tile drains have been and are being installed to carry the saline water away from the fields. However, there have been adverse environmental effects associated with this wastewater.

In 1982, the U.S. Fish and Wildlife Service discovered selenium concentrations in fish from the San Luis Drain and Kesterson Reservoir to be as much as 100 times higher than background. It also found high mortalities and deformities among newborn coots, grebes, stilts, and ducks.

There was early concern about the potential for impacts on beneficial uses in the Estuary if the Drain were completed and discharged into the Delta. In response, the Water Board prohibited the proposed discharge in 1964, unless compelling evidence that the proposed discharge would not harm beneficial uses was submitted by proponents. In 1981, the Water Board requested that the State Board take the lead role in developing, revising, renewing, and enforcing waste discharge requirements for the Drain.

Unfortunately, the problem of agricultural drainage still exists. The San Joaquin Valley Drainage Program, another state and federal interagency program, has begun to investigate further the problems associated with the drainage of agricultural lands and to develop solutions.


Protection of beneficial uses associated with the Estuary also depends upon achieving water quality goals within each of the watersheds draining to the Bay. Successful wasteload allocations depend upon limiting pollutant influx from nonpoint as well as point sources. In turn, nonpoint source control is dependent on a wide range of factors, including physical factors such as the geology and hydrological characteristics of an area; existing natural resources such as vegetation along streambanks; and a wide range of human activities.

Watershed management planning in each countywide program or individual watershed involves a series of steps. First, a detailed assessment of current conditions, including identification of existing or potential problems, is conducted. Next, the process attempts to bring together all affected stakeholders and interested parties to determine how they would manage their watershed. Finally, specific actions are taken during implementation of the countywide or local watershed action plan.

The Water Board firmly believes that watershed planning and protection efforts will not be effective unless solutions are defined and implemented at the local level. The following sections present four examples of local watershed management planning activities supported by the Water Board. THE NAPA RIVER WATERSHED

The Water Board has initiated county-level watershed management planning efforts. The first began in the Napa River Watershed where depressed oxygen levels, high coliform levels, and sedimentation due to erosion were recurring problems in segments of the Napa River.

The Water Board initiated the planning process by preparing a complete resource evaluation in cooperation with a wide range of local public and private entities. This evaluation encompassed traditional evaluations of natural resources and also included descriptions of existing management and regulatory frameworks, funding, and tax incentive programs to support the local planning process.

The Water Board is supporting local agency staff, public officials, agricultural landowners, urban residents of Napa County, and the Napa Resource Conservation District in their efforts to define watershed management goals and specific actions that will eventually allow those goals to be met. In 1999, the Water Board issued waste discharge requirements (WDRs) for the Napa River Flood Control Project, which has set a national standard for innovative, community-based planning to ensure a "Living River" corridor along the Napa River that protects water quality, successfully integrating flood control, water quality, and habitat protection requirements. THE SANTA CLARA BASIN WATERSHED MANAGEMENT INITIATIVE

In 1996, the Water Board and the U.S. EPA initiated a broad stakeholder effort to encourage local stewardship in the Santa Clara basin as part of the statewide WMI. The Santa Clara basin is defined as the San Francisco Bay south of the Dumbarton Bridge and the watersheds draining to that segment of the Bay. The Santa Clara Basin Watershed Management Initiative is a broad-based stakeholder group of 32 signatories from local, state and federal public agencies, business and trade associations, and civic and environmental groups and programs. The declared purpose of this WMI is "to develop and implement a comprehensive watershed management program - one that recognizes that healthy watersheds mean addressing water quality problems and quality of life issues for the people, animals and plants that live in the watershed." This WMI first established a mission statement, goals, planning objectives for development of a watershed action plan, implementation objectives, and a framework for conducting a watershed assessment. The most outstanding successes of this WMI have been in sustaining organizational continuity, providing a forum for stakeholder input on regulatory actions, and producing a variety of outreach materials for the general public to assist in natural resource protection. This WMI has continued to develop its foundation by producing watershed assessments (2002), and a watershed action plan (2003), and by further developing its priorities for implementation to protect and improve water quality (2005). THE TOMALES BAY WATERSHED

The Tomales Bay watershed in western Marin County is one of the major estuaries on the west coast of the United States. It has a diverse ecosystem and several notable tributaries, including Lagunitas Creek, which has one of the few remaining viable coho salmon runs in central California. In December 1999, the local citizens and state, federal, and local agencies formed the Tomales Bay Watershed Council. The Council produced a Stewardship Plan for the Tomales Bay watershed to ensure that water quality in Tomales Bay and its tributary streams is sufficient to support natural resources and beneficial uses. The plan also includes recommendations to restore and protect the integrity of natural habitats and native plant communities, which contribute to improved water quality. The Water Board has actively participated on the Council, working with the other agencies and interested parties to coordinate monitoring and recommend funding for grant projects for a variety of pollution prevention and restoration projects within the watershed. THE CONTRA COSTA WATERSHED FORUM

The Contra Costa Watershed Forum (CCWF) was established as a result of a countywide Creek and Watershed Symposium in 1999. The CCWF is an open committee of approximately 50 organizations, including federal, state, and local agencies; local governments; a professional watershed research organization; local non-profit environmental and education organizations; community volunteer groups; and private citizens. The CCWF staff are from the Contra Costa County Community Development Department. This diverse group of stakeholders is united by their concern for the watersheds of Contra Costa County. Through the coordinated activities of the CCWF, local creek and watershed groups have been sustained, and the CCWF has received grant funding for creek surveys and mapping, biological water quality (benthic macroinvertebrate) monitoring, and production of the Watershed Atlas. The Watershed Atlas compiles information on geography, hydrology, demographics, impervious surface, drainage patterns and much other information pertinent to water quality protection and evaluation, including activities of local watershed groups and restoration projects. The Water Board supports the CCWF by attendance at meetings, management of grant-funded projects, and work with CCWF staff on setting watershed priorities. These efforts are leading to water quality improvements as the citizens of Contra Costa County become more directly involved in assessing, monitoring, restoring, and protecting their watersheds.


To protect water quality of all aquatic systems throughout the region, the discharge prohibitions listed in Table 4-1 apply. The Water Board will not allow exceptions to these prohibitions, except where noted below.

Exceptions to Prohibitions 1, 2, and 3 will be considered where:

  • An inordinate burden would be placed on the discharger relative to beneficial uses protected and an equivalent level of environmental protection can be achieved by alternate means, such as an alternative discharge site, a higher level of treatment, and/or improved treatment reliability; or
  • A discharge is approved as part of a reclamation project; or
  • It can be demonstrated that net environmental benefits will be derived as a result of the discharge; or
  • A discharge is approved as part of a groundwater clean-up project, and in accordance with Resolution No. 88-160 "Regional Board Position on the Disposal of Extracted Groundwater from Groundwater Clean-up Projects," and it has been demonstrated that neither reclamation nor discharge to a POTW is technically and economically feasible, and the discharger has provided certification of the adequacy and reliability of treatment facilities and a plan that describes procedures for proper operation and maintenance of all treatment facilities. (The Water Board recognizes the resource value of extracted and treated groundwater and urges its utilization for the highest beneficial use for which applicable water quality standards can be achieved.)

In reviewing requests for exceptions, the Water Board will consider the reliability of the discharger's system in preventing inadequately treated wastewater from being discharged to the receiving water and the environmental consequences of such discharges.

Prohibitions 1 through 5 refer to particular characteristics of concern to beneficial uses. The Water Board may consider an exception to 4 provided that any proposed reclamation project demonstrates that beneficial uses will be protected. This broad language has been and will be interpreted by the Water Board on a case-by-case basis. It should be noted that the Water Board will consider all discharges of treated sewage and other discharges where the treatment process is subject to upset to contain particular characteristics of concern unless the discharger can demonstrate that the discharge of inadequately treated waste will be reliably prevented.


The detailed program descriptions presented in the remainder of this chapter are focused on protecting water quality in systems ranging from small creeks to the larger Estuary.

The section on point source control focuses primarily on protecting beneficial uses in each segment of the Estuary, as well as the whole system. The section on nonpoint source control focuses primarily on individual watersheds, but also on the contributions of runoff to the larger Bay system. The section on groundwater protection and management centers on groundwater basins within each watershed. The section on emerging program areas describes resources and issues that have increasingly become the focus of Water Board activity. Often, these areas require integrated and innovative approaches that are substantially different than those that exist in established programs.


Surface waters in the region consist of inland surface water (freshwater lakes, rivers, and streams), estuaries, enclosed bays, and ocean waters. Historical and ongoing wasteloads contributed to the surface water bodies in the region come from upstream discharges carried into the region via Delta outflow, direct input in the forms of point and nonpoint sources, and indirect input via groundwater seepage.

A point source usually refers to waste emanating from a single, identifiable location, while a nonpoint source usually refers to waste emanating from diffuse locations. While legally considered point sources, stormwater sewer systems are discussed under the nonpoint source control because waste entering the systems is generated from diffuse sources. This section describes control measures for point source discharges. The Water Board may control either type of discharge, but approaches may differ.

Wasteloads from point sources are those that are generally associated with pollutant discharges from an identifiable location to a specific receiving water body. Major types of point sources include:

  • Treated municipal sewage discharged from Publicly Owned Treatment Works (POTWs), which often consist of a combination of domestic, industrial, and commercial waste streams;
  • Treated industrial wastewater resulting from industrial operations, processing, cleaning, and cooling;
  • Treated groundwater from clean-up of groundwater pollution sites; and,
  • Other miscellaneous types of discharges, including certain non-point sources with a physically identifiable point of discharge.


Point source discharges to surface waters are generally controlled through waste discharge requirements issued under the federal National Pollutant Discharge Elimination System (NPDES) permits. Although the NPDES program was established by the federal Clean Water Act, the permits are prepared and enforced by the Water Boards per California's delegated authority for the act.

Issued in five-year terms, an NPDES permit usually contains components such as discharge prohibitions, effluent limitations, and necessary specifications and provisions to ensure proper treatment, storage, and disposal of the waste. The permit often contains a monitoring program that establishes monitoring stations at effluent outfall and receiving waters.

Under the state's Porter-Cologne Water Quality Control Act, any person discharging or proposing to discharge waste within the region (except discharges into a community sewer system) that could affect the quality of the waters of the state is required to file a Report Of Waste Discharge (ROWD). The Water Board reviews the nature of the proposed discharge and adopts Waste Discharge Requirements (WDRs) to protect the beneficial uses of waters of the state. Waste discharge requirements could be adopted for an individual discharge, or a specific type of discharges in the form of a general permit. The Water Board may waive the requirements for filing a ROWD or issuing WDRs for a specific discharge where such a waiver is not against the public interest. NPDES requirements may not be waived.

Acceptable control measures for point source discharges must ensure compliance with NPDES permit conditions, including the discharge prohibitions (Table 4-1) and the effluent limitations provided on the following pages. In addition, control measures must satisfy water quality objectives set forth in the Basin Plan unless the Water Board judges that related economic, environmental, or social considerations merit a modification after a public hearing process has been conducted. Control measures employed must be sufficiently flexible to accommodate future changes in technology, population growth, land development, and legal requirements.



The federal Clean Water Act (CWA) requires that NPDES permits include technology-based and, where appropriate, water quality-based effluent limitations. Technology-based effluent limitations are promulgated performance standards based on secondary treatment or best practicable control technology. When technology-based limitations fail to attain or maintain acceptable water quality (as measured by water quality objectives) or comply with water quality control plans, additional or more stringent effluent limitations will be required in order to attain water quality objectives. The more stringent limitations are known as water quality-based limits.

Water quality-based effluent limitations will consist of narrative requirements and, where appropriate, numerical limits for the protection of the most sensitive beneficial uses of the receiving water. Establishing numeric limits takes into account the appropriate water quality objectives, background concentrations in the receiving water, and allowable dilution credit.

In many cases, numerical water quality objectives are not available for various types of beneficial uses or for various constituents of concern. In these cases, best professional judgment will be used in deriving numerical effluent limitations that will ensure attainment and maintenance of narrative water quality objectives.


In some cases, the Water Board may elect to develop and adopt site-specific water quality objectives. These objectives will reflect site-specific conditions and comply with the Antidegradation Policy. This situation may arise when:

  • It is determined that promulgated water quality standards or objectives are not protective of beneficial uses; or
  • Site-specific conditions warrant less stringent effluent limits than those based on promulgated water quality standards or objectives, without compromising the beneficial uses of the receiving water.

In the above cases, the Water Board may consider developing and adopting site-specific water quality objectives for the constituent(s) of concern. These site-specific objectives will be developed to provide the same level of environmental protection as intended by national criteria, but will more accurately reflect local conditions. Such objectives are subject to approval by the State Board, Office of Administrative Law, and U.S. EPA.

There may be cases where the promulgated water quality standard or adopted objectives are practically not attainable in the receiving water due to existing high concentrations. In such circumstances, discharges shall not cause impairment of beneficial uses.

Site-specific objectives have been adopted by the Water Board for copper in San Francisco Bay and for nickel in South San Francisco Bay, (Table 3-3A) and for cyanide in San Francisco Bay (Table 3-3c).


In developing and setting water quality-based effluent limitations for toxic pollutants, best professional judgment will involve consideration of many factors. Factors that may be considered include:

  • Applicable and relevant federal laws, regulation, and guidance (specifically 40 CFR122 and 131, promulgated National Toxics Rules, U.S. EPA Water Quality Criteria, and technical guidance on water-quality based toxics control);
  • State laws, regulations, policies, guidance, and Water Quality Control Plans;
  • This Regional Water Quality Control Plan;
  • Achievability by available technology or control strategies;
  • Effectiveness of pollution prevention and source control measures; and
  • Economic and social costs and benefits.

While the conditions surrounding a waste discharge may vary from case to case, all attempts will be made to ensure consistency among permits when exercising best professional judgment.

The effluent limitations described below have been established to help achieve the water quality objectives identified in Chapter 3.

Numerical effluent limitations identified in this section may not contain a complete list of pollutants that have a reasonable potential to cause an adverse impact on water quality. Inclusion of such pollutants of concern into the NPDES permit will be evaluated on a case-by-case basis.

The Water Board will consider establishing more stringent limitations as necessary to meet water quality objectives and protect beneficial uses in particularly sensitive areas. Similarly, the Water Board will consider establishing less stringent limitations, consistent with state and federal laws, for any discharge where it can be conclusively demonstrated through a comprehensive program approved by the Water Board that such limitations will not result in unacceptable adverse impacts on the beneficial uses of the receiving water. Such a comprehensive program must evaluate the impact of other, nearby discharges as well as the discharge itself.

The numerical limits identified in this section have been and will be applied on a gross rather than a net basis except for certain industrial waste discharges, which will be evaluated on a case-by-case basis.


Within the context of this Basin Plan, ocean waters of the region are all territorial marine waters of the state west of the coastline, except enclosed bays.

All discharges to ocean waters must comply with the applicable quality requirements for waste discharges specified in the State Board's Ocean Plan and Thermal Plan.


Within the context of this plan, enclosed bays are the indentations along the coast that enclose an area of marine water (such as Tomales Bay and Drake's Estero) including San Francisco Bay; estuaries extend from a bay to points upstream where there is no significant mixing or fresh water or sea water (this includes significant portions of the main San Francisco Bay and the portions of streams draining to the Bay where salt and freshwater mix); and inland surface waters are all other waterbodies within the region (freshwater rivers, streams, lakes, and reservoirs). As described in Chapter 3, effluent limits for discharge into any surface water body within the region is based on salinity. These are defined in the State Enclosed Bays and Estuaries Policy, 1974. LIMITATIONS FOR CONVENTIONAL POLLUTANTS

Table 4-2 contains effluent limitations for discharges to inland surface waters and enclosed bays and estuaries within the region.

Table 4-2a contains effluent limitations for bacteriological indicator organisms. All NPDES permits for discharges that contain sanitary waste shall include the applicable effluent limitations from Table 4-2a, except for discharges into Hayward Marsh, for which REC-1 is not a designated beneficial use. The water quality-based effluent limitations in Table 4-2a may be adjusted to account for dilution in a manner consistent with procedures in the Policy for Implementation of Toxics Standards for Inland Surface Waters, Enclosed Bays, and Estuaries of California. LIMITATIONS FOR SELECTED TOXIC POLLUTANTS

Water quality-based effluent limitations for shallow water and deepwater dischargers shall be calculated according to the methodology in the “Policy for Implementation of Toxics Standards for Inland Surface Waters, Enclosed Bay, and Estuaries of California (SIP).” and any amendments thereto.

The Water Board may adopt additional numerical standards for conservative constituents documented in discharges and/or documented to be of concern in receiving waters. WHOLE EFFLUENT TOXICITY LIMITS AND CONTROL PROGRAM

The narrative water quality objective for toxicity (see Chapter 3) protects beneficial uses against mixtures of pollutants typically found in aquatic systems. This approach is used because numerical objectives for individual pollutants do not take mixtures into account and because numerical objectives exist for only a small fraction of potential pollutants of concern.

Effluent limits for acute toxicity are described below and were derived through the Effluent Toxicity Characterization Program (ETCP). A detailed description of the ETCP is presented later in this section. These limits define in specific terms how the Water Board assesses whether waters are "maintained free of toxic substances in concentrations that are lethal to or that produce other detrimental responses in aquatic organisms" (the narrative objective in Chapter 3) and maintains waters free of "toxic substances in toxic amounts" (Clean Water Act). ACUTE TOXICITY

The acute toxicity effluent limitation states that the survival of organisms in effluent shall be a median value of not less than 90 percent survival, and a 90 percentile value of not less than 70 percent survival using tests as specified in Table 4-4 and Table 4-5.

Compliance with the acute toxicity limitation is evaluated by measuring survival of test fishes exposed to effluent for 96 hours. Each fish species represents a single sample. Dischargers are required to conduct flow-through effluent toxicity tests, except for those that discharge intermittently and discharge less than 1.0 million gallons per day (average dry weather flow). Such small, intermittent dischargers are required to perform static renewal bioassays.

All dischargers perform toxicity tests using fish species, according to protocols approved by the U.S. EPA or State Board or published by the American Society for Testing and Materials (ASTM) or American Public Health Association. Two fish species shall be tested concurrently. These shall be the most sensitive two species determined from concurrent screening(s) of three species: three-spine stickleback, rainbow trout, and fathead minnow. Tests completed within ten days of the initial test are considered concurrent. This three-species-screening requirement can be met using either flow-through or static renewal bioassays.

The Water Board may consider allowing compliance monitoring with only one (the most sensitive, if known) fish species, if the following condition is met: The discharger can document that the acute toxicity limitation, specified above, has not been exceeded during the previous three years, or that acute toxicity has been observed in only one of two fish species.

The Water Board may modify the flow-through bioassay requirements and the specific test species requirements on a case-by-case basis for discharges of once-through cooling water or excessively saline wastes, which make the implementation of these test requirements impractical. Such changes are not intended as a reduction in the acute toxicity limitation, but rather to account for the technical difficulties of performing the tests.

In addition, for deep water discharges subject to marine effluent limitations, dischargers are not to be considered out of compliance with the acute toxicity effluent limitation under the following circumstances: the discharger documents that the only cause of acute toxicity is ammonia which rapidly decays in the receiving water, and demonstrates that ammonia in the discharge does not impact water quality or beneficial uses. CHRONIC TOXICITY

Chronic toxicity effluent limits are derived for individual dischargers based upon Best Professional Judgement. Some of the factors that may be considered in the development of these limits include: allowing credit for dilution comparable to those allowed for numeric chemical-specific objectives, effluent variability, and intent to protect against consistent chronic toxicity and severe episodic toxic events.

Chronic toxicity limitations are contained in the permits of all dischargers that have completed or are currently participating in the Effluent Toxicity Characterization Program (ETCP). This includes all municipal facilities with pre-treatment programs, all major industrial facilities, and selected treated groundwater dischargers.

Monitoring requirements for chronic toxicity, such as test species, effluent sampling procedures, dilution series, monitoring frequency, dilution waters and reference toxicant testing requirements, are specified in NPDES permits on a case-by-case basis. Monitoring requirements will be based on Effluent Toxicity Characterization Program data. Test species and protocols will be selected from those listed in Table 4-5.

Dischargers with chronic toxicity limits in their permits monitoring quarterly or less frequently are required to accelerate the frequency to monthly (or as otherwise specified by the Executive Officer) when conditions such as those listed in Table 4-6 occur. TOXICITY IDENTIFICATION/REDUCTION EVALUATION (TIE/TRE)

Permits shall require that if consistent toxicity is exhibited, then a chronic toxicity identification evaluation (TIE) and toxicity reduction evaluation (TRE) shall be conducted. Specific language in permits requires the development of workplans for implementing TIEs. TIEs will be initiated within 30 days of detection of persistent toxicity. The purpose of a TIE is to identify the chemical or combination of chemicals causing the observed toxicity. Every reasonable effort using currently available TIE methodologies shall be employed by the discharger. The Water Board recognizes that identification of causes of chronic toxicity may not be successful in all cases.

The purposes of a TRE are to identify the source(s) of the toxic constituents and evaluate alternative strategies for reducing or eliminating their discharge. The TRE shall include all reasonable steps to reduce toxicity to the required level. In addition, the Water Board will review chronic toxicity test results to assess acute toxicity and consider the need for an acute TIE.

Following completion of the TRE, if consistent toxicity is still exhibited in a discharge, then the discharger shall pursue all feasible waste minimization measures at a level that is acceptable to the Water Board. The discharger must document that the acceptable level of participation is maintained by submitting reports on a specified schedule to the Water Board.

A Toxicity Reduction Evaluation may again be required in situations where chronic toxicity still exists and new techniques for identifying and reducing toxicity become available. Alternatively, the cause of effluent toxicity may change, so that existing techniques will enable identification and reduction of toxicity.

Consideration of any enforcement action by the Water Board for violation of the effluent limitation will be based in part on the discharger's actions in identifying and reducing sources of persistent toxicity. EFFLUENT TOXICITY CHARACTERIZATION PROGRAM

The Effluent Toxicity Characterization Program was initiated in 1986 with the goal of developing and implementing toxicity limits for each discharger based on actual characteristics of both receiving waters and waste streams. The Water Board initiated the program as a means of implementing the narrative objective prohibiting toxic effects in receiving water.

The first two phases of the program focused on developing methods for monitoring effluent toxicity (known as effluent characterization) and deriving the appropriate series of tests to ensure that each effluent and its immediate receiving waters are not toxic to aquatic organisms.

Information from these phases is used to determine whether the narrative objectives are being met in each segment of the Bay and will support the development of site-specific water quality objectives and wasteload allocations.

As the program progresses, the Water Board may: (a) Modify existing effluent limits; (b) Specify different test organisms and methods for determining compliance with toxicity effluent limits; and/or (3) Require a toxicity reduction evaluation (TRE) to determine the cost-effectiveness of controlling toxicity or reducing concentrations of specific pollutants.

This program is being implemented within the existing framework of the NPDES permitting program for municipal and industrial facilities.

The purposes of effluent characterization are to:

  • Define effluent variability so that the most appropriate compliance monitoring program can be put in place for each discharge and so that adequate information can be developed to determine if treatment processes or source control modifications are necessary to comply with effluent limits;
  • Define the sensitivity of different test species to different effluents so that appropriate acute toxicity effluent limits can be defined and to identify the most sensitive of a group of test organisms used for compliance monitoring; and
  • Define the chronic toxicity of the effluent to different test species such that the most sensitive organism of a standard set can be defined and either used for compliance monitoring or used for development of application factors to be applied to the acute toxicity effluent limit.

Two rounds of effluent characterization have been completed by dischargers selected on the basis of the nature, volume, and location of discharge. The first round started characterization in 1988; the second round in 1991. The Water Board adopted guidance documents for each round of characterization, with modifications made to the second round from knowledge gained during the first. Status reports were issued in July, 1989, March, 1990, and July, 1991. A summary report is scheduled upon completion of the second round in 1995. The need for a third round of characterization will be evaluated at that time.

Thus far, no one test species has consistently been the most sensitive to all discharges. This strongly supports the current approach of requiring screening using several test species. Also, acute toxicity has been observed at several sites using the expanded range of test species.

Although these sites can meet existing limits with test species currently used to determine compliance (fathead minnow, trout, and stickleback), they cannot meet the limits based on more sensitive species now available.

Detailed technical guidelines for conducting toxicity tests and analyzing resulting data were compiled in "Modified Guidelines: Effluent Toxicity Characterization Program," San Francisco Bay Regional Water Quality Control Board, 1991, Resolution No. 91-083, after experience gained during the first round. This document is incorporated by reference into this plan.



The allocation of dilution ratio depends on whether a discharge is classified as a deep water or a shallow water discharge. In order to be classified as a deep water discharge, waste must be discharged through an outfall with a diffuser and must receive a minimum initial dilution of 10:1, with generally much greater dilution. All other dischargers are classified as shallow water discharges. DEEP WATER DISCHARGES

While it is recognized that the actual initial dilution of many deep water discharges is greater than ten, the Water Board has taken a conservative approach to calculating effluent limitations for the following reasons. First, there is concern over the effects of the cumulative mass loadings of toxic pollutants from the numerous discharges into San Francisco Bay. Limiting the allocation of dilution credits is one means of limiting mass loadings. Second, recent Water Board studies have detected toxicity in ambient waters throughout the Bay system based on laboratory toxicity tests. This calls for a cautious approach in allowing the discharge of toxic substances. Third, studies indicate that bioaccumulation of pollutants in San Francisco Bay biota is of concern to wildlife and human health. Fourth, it is difficult to either measure or predict actual dilution in the San Francisco Bay estuarine environment. In the Estuary, the direction of waste transport varies over the course of the tidal cycle, so it is difficult to determine the fraction of new water versus recirculated water mixing with the discharge. U.S. EPA has developed several models of initial dilution for discharge plumes, but none take into account transport due to tidal currents.

The Water Board will consider inclusion of an effluent limitation greater than that calculated from water quality objectives when the increase in concentration is caused by implementation of significant water reclamation or water reuse programs at the facility; the increase in the effluent limitation does not result in an increase in the mass loading; and water quality objectives will not be exceeded outside the zone of initial dilution. SHALLOW WATER DISCHARGES

Shallow water dischargers are subject to a discharge prohibition (Table 4-1, No. 1), which is intended to protect beneficial uses in areas that receive very limited, if any, dilution. When an exception to the prohibition is granted, it is generally not appropriate to allocate dilution credits for purposes of calculating effluent limitations, because these shallow aquatic environments are often biologically sensitive or critical habitats.

However, dilution credit may be granted on a discharger-by-discharger and pollutant-by-pollutant basis based on provisions of the “Policy for Implementation of Toxics Standards for Inland Surface Waters, Enclosed Bay, and Estuaries of California (SIP).” In making this determination, the Water Board will grant dilution credit on a pollutant-by-pollutant basis if the discharger demonstrates that an aggressive pretreatment and source control program is in place, including the following:

  • Completion of a source identification study;
  • Development and implementation of a source reduction plan; and
  • Commitment of resources to fully implement the source control and reduction plan.

Any dilution credit granted must be consistent with the antibacksliding policy and may be granted only after very rigorous scrutiny of source control efforts and receiving water data. When dilution is granted, permits shall include provisions requiring continuing efforts at source control, targeting the substances to which the exceptions apply.

For certain low volume, short duration, or one-time discharges, the requirements of pretreatment and source control programs may not be practical. The Water Board may choose to waive such requirements for pollutants in low volume discharges determined to have no significant adverse impact on water quality.

In addition, the Water Board will consider the discharger's demonstration of compliance with water quality objectives, in accordance with the SIP. This demonstration shall address the following issues:

(a) A demonstration that the proposed effluent limitation will result in compliance with water quality objectives, including the narrative chronic toxicity objective, in the receiving water. Water quality objectives used in this demonstration are to be based on ambient salinity and hardness (for fresh waters) at the time of sampling. In addition, demonstration of compliance is to be based on the averaging period associated with each objective. Compliance with both acute and chronic chemical-specific water quality objectives shall be demonstrated. If freshwater objectives apply in the receiving waters (i.e., salinity is less than 5 parts per thousand), compliance with saltwater objectives shall also be demonstrated at the nearest point in the receiving waters where salinity reaches 5 parts per thousand. Such a demonstration shall be based on ambient monitoring at a frequency equal to that typically required for effluent monitoring for a period of time defined in the study plan;

(b) An evaluation of worst-case conditions (in terms of tidal cycle, currents, or instream flows, as appropriate) through monitoring and/or modeling to demonstrate that water quality objectives will continue to be met, taking into account the averaging period associated with each objective; and

(c) An evaluation of the effects of mass loading resulting from allowing higher concentrations of pollutants in the discharge, in particular, the potential for accumulation of pollutants in aquatic life or sediments to levels that would impair aquatic life or threaten human health. This evaluation may include sampling of sediment and biota in the vicinity of the discharge to determine the accumulation of pollutants resulting from the current levels of discharge.

A study plan for conducting this work must be submitted to the Water Board for approval by the Executive Officer. Results of the study or studies addressing these three points shall be submitted to the Water Board. Effluent limitations based on either concentration or mass loading shall be developed for consideration by the Water Board based on study results and any other available information. The goal in setting effluent limitations shall be to ensure that water quality objectives are met in the receiving water and that mass loadings are limited to a level that provides protection of beneficial uses. In no case shall effluent limitations impair the basis upon which exception to the prohibition against discharge to shallow water was granted. Continued ambient monitoring shall also be required to ensure that water quality objectives are met.


Due to the unique estuarine environment that exists in the region, the salinity characteristics (i.e., freshwater vs. marine water) of the receiving water shall be considered in establishing water quality objectives. Freshwater effluent limitations shall apply to discharges to waters both outside the zone of tidal influence and with salinities equal to or less than 1 part per thousand at least 95 percent of the time in a normal water year. Marine effluent limitations shall apply to discharges to waters with salinities equal to or greater than 10 parts per thousand at least 95 percent of the time, except for discharges to the Pacific Ocean, which are covered by the California Ocean Plan. For discharges to waters with salinities in between these two categories, defined as estuarine, effluent limitations shall be the lower of the marine or freshwater effluent limitation, based on ambient hardness, for each substance. The use of alternative marine or freshwater criteria may be approved if scientifically defensible information and data demonstrate that on a site-specific basis the biology of the water body is dominated by freshwater aquatic life; or conversely, the biology of the water body is dominated by marine aquatic life.


When dilution credit is granted, the background concentration of the substance is taken into account in calculating effluent limitations so that the dilution provided by mixing with receiving waters is not overestimated. Ambient background concentration means the concentration of a substance, in the vicinity of a discharge, which is not influenced by the discharge. For the San Francisco Estuary, it is difficult to identify a location that is not influenced by a discharge. Furthermore, background concentrations should vary within the Estuary due to changing geochemistry of the waters as they travel downstream. However, in order to simplify the calculation of effluent limitations, it is desirable to use one background concentration throughout the region.

The determination of ambient background concentration, for purposes of establishing NPDES effluent limitations for toxic pollutants, will be done in accordance with the provisions of the SIP, and amendments thereto.


In incorporating and implementing effluent limitations in NPDES permits, the following general guidance shall apply:


Where water quality objectives in the receiving water are being met, and an existing effluent limitation for a substance in a discharge is significantly lower than appropriate water quality-based limits, performance-based effluent limitations for that substance may be specified or the effluent limit revised. Any changes are subject to compliance with the state Antidegradation Policy. The performance-based effluent limitation may be either concentration- or mass-based, as appropriate.


Once the Water Board has adopted a site-specific objective for any substance, effluent limitations shall be calculated from that objective in accordance with the methodology in the “Policy for Implementation of Toxics Standards for Inland Surface Waters, Enclosed Bays, and Estuaries of California” (SIP).

Site-specific objectives have been adopted by the Water Board for copper in San Francisco Bay and for nickel in South San Francisco Bay (Table 3-3A) and for cyanide in San Francisco Bay (Table 3-3C). COPPER AND NICKEL IN SOUTH SAN FRANCISCO BAY
As part of the implementation plan for copper and nickel site-specific objectives, the municipal wastewater dischargers in South San Francisco Bay shall have effluent limits for copper and nickel, derived from the site-specific objectives in Table 3-3A using SIP methodology. The Water Quality Attainment Strategy for copper and nickel in South San Francisco Bay that implements these site-specific objectives is included in Chapter 7. CYANIDE
Cyanide is present in low levels in all municipal wastewater effluents and most industrial wastewater effluents. Disinfection processes contribute to in-plant formation of cyanide. Therefore, cyanide in the effluent from municipal treatment plants is a combination of cyanide in the influent and cyanide produced during disinfection. Cyanide concentration spikes in the effluent, although rare, are generally caused by accidental high concentration discharges in the collection system.

As part of the implementation plan for marine site-specific objectives for cyanide, all municipal wastewater dischargers that discharge to any segment of San Francisco Bay including Sacramento/San Joaquin River Delta (within San Francisco Bay region), Suisun Bay, Carquinez Strait, San Pablo Bay, Central San Francisco Bay, Lower San Francisco Bay, and South San Francisco Bay shall have effluent limits for cyanide derived from the marine site-specific objectives in Table 3-3C, using the methodology in the SIP. Specifically, under Step 7 of the SIP methodology, effluent limits are necessary considering the nature of cyanide, its use in the disinfection process, and to promote achievement and ensure maintenance of the marine cyanide site-specific objectives.

Industrial wastewater dischargers to San Francisco Bay shall have effluent limits for cyanide derived from the marine site-specific objectives in Table 3-3C, using the methodology in the SIP. However, effluent limits shall not be required, under Step 7 of the SIP alone, where the industrial discharger demonstrates one of the following:

  • Cyanide is not detected in its effluent, using a method with a detection limit of 1.0 µg/l
  • It does not disinfect any portion of its effluent
  • It otherwise demonstrates that cyanide is not used in its industrial process
Effluent limits for shallow water dischargers that have been granted an exception to Basin Plan Prohibition 1 shall be based on the dilution credits set forth in Table 4-6. Setting forth dilution credits in Table 4-6 does not authorize discharges into shallow waters. Each discharger must continue to satisfy all requirements for an exception to Basin Plan Prohibition 1.

Where cyanide effluent limits are included in an NPDES permit, the discharger shall be required to implement a monitoring and surveillance program. This program shall include influent and effluent monitoring and ambient monitoring in San Francisco Bay. Each discharger shall review sources of cyanide to its influent at least once every five years. Where potential cyanide contributors exist within a discharger's service area, the discharger shall implement a local program to prevent illicit discharges to the sewer system which, at a minimum, shall include inspecting potential contributor sites, developing and distributing educational materials and preparing emergency monitoring and response plans to be implemented if a significant cyanide discharge occurs. Additionally, if ambient monitoring shows cyanide concentrations of 1.0 µg/L or higher, the discharger shall undertake actions to determine and abate identified sources of cyanide in San Francisco Bay.


For some substances there may be more than one effluent limitation with different averaging periods (e.g., daily average and 30-day average). In both cases, the effluent limitations shall apply to the mean concentration of all samples analyzed during the averaging period. If only one sample is taken during the averaging period, the effluent limitation applies to the concentration of that sample.


Method Detection Limits are defined in Title 40, Code of Federal Regulations, Part 136, Appendix B (revised June 30, 1986).

Practical Quantitation Level is the lowest concentration of a substance within plus or minus 20 percent of the true concentration by 75 percent of the analytical laboratories testing in a performance evaluation study. If performance data are not available, the PQL is the MDL x 5 for carcinogens and the MDL x 10 for noncarcinogens.

Limits of Quantification are ten standard deviations greater than the average measured blank values used in developing the MDL.

These terms and concepts are useful when pollutant concentrations in waters are relatively low. However, these will be taken into account in determining compliance with, rather than in the calculation of, effluent limitations.


Effluent limits are not necessary for substances that do not pose any risk to beneficial uses or are shown not to be present in discharge. However, a discharger must demonstrate to the satisfaction of the Water Board that particular substances do not cause, or have the reasonable potential to cause or contribute to an excursion above numerical and narrative objectives. Dischargers must also demonstrate that pollutants of concern are (a) not in the waste stream, and (b) no change has occurred that may cause release of pollutants. This certification shall be supported, at a minimum, by monitoring results for such pollutants and process and treatment descriptions that demonstrate these substances are not expected to be present in the waste stream. At a minimum, this monitoring and certification is required prior to issuance and reissuance of WDRs.

The Water Board may choose to not require periodic monitoring and certification for pollutants in low volume discharges determined to have no significant adverse impact on water quality.


As new objectives or standards are adopted, permits will be revised accordingly. Revised permits will distinguish between effluent limitations that are met by current performance, and effluent limitations not currently attained. Immediate compliance will be required for effluent limitations that are met by current performance.

The Water Board may consider dischargers' proposals for longer compliance schedules for newly adopted objectives or standards as NPDES permit conditions for particular substances, where revised effluent limitations are not currently being met and where justified. The primary goal in setting compliance schedules is to promote the completion of source control and waste minimization measures, including water reclamation.

Justification for compliance schedules will include, at a minimum, all of the following:

(a) Submission of results of a diligent effort to quantify pollutant levels in the discharge and the sources of the pollutant in the waste stream;

(b) Documentation of source control efforts currently underway or completed, including compliance with the Pollution Prevention program described in the Basin Plan;

(c) A proposed schedule for additional source control measures or waste treatment; and

(d) A demonstration that the proposed schedule is as short as possible.

Implementation of source control measures to reduce pollutant loadings to the maximum extent practicable shall be completed as soon as possible, but in no event later than four years after new objectives or standards take effect. Implementation of any additional measures that may be required to comply with effluent limitations shall be completed as soon as possible, but in no event later than ten years after new objectives or standards take effect. The issuance of the permit containing a compliance schedule should not result in a violation of any applicable requirement of the federal Clean Water Act or the California Water Code, including any applicable Clean Water Act statutory deadlines.


As discussed in a later section titled "Urban Runoff Management," the Water Board has initiated a program that regulates certain municipal, industrial, and construction stormwater discharges through NPDES permits. Since both the sources of pollutants in stormwater discharges and the points of discharge are diffuse, and the methods of reducing pollutants in stormwater discharges are in the development stage, water quality-based numerical effluent limitations are not feasible at this time. Instead, stormwater permits will include requirements to prevent or reduce discharges of pollutants that cause or contribute to violations of water quality objectives. Compliance with these requirements is expected to be achieved through implementation of control measures or best management practices identified in dischargers' stormwater management plans or stormwater pollution prevention plans. Instead, stormwater permits will include requirements to prevent or reduce discharges of pollutants that cause or contribute to violations of water quality objectives for receiving waters. Compliance with these requirements is expected to be achieved through implementation of control measures or best management practices identified in dischargers' stormwater management plans or stormwater pollution prevention plans.

The Water Board is taking a phased approach towards attainment of water quality objectives in waters that receive stormwater discharges from urban areas and certain industrial and construction activities. The Water Board will first require entities subject to NPDES permits for stormwater discharges to complete implementation of technically and economically feasible control measures to reduce pollutants in stormwater to the maximum extent practicable. For industrial facilities, such control measures include those representing the best available technology that is economically achievable.

NPDES permits for stormwater discharges will require completion of technically and economically feasible control measures as soon as possible. Specific schedules for implementing control measures may, at the discretion of the Water Board, be included in permits (to the extent that such schedules are authorized by state or federal laws) either by reference to a stormwater management plan or by permit conditions. In no event will these schedules extend beyond the term of the permit.

If this first phase does not result in attainment of water quality objectives, the Water Board will consider permit conditions which may require implementation of additional control measures. In such circumstances, the Water Board may consider dischargers' proposed schedules for identification and implementation of additional control measures designed to attain water quality objectives. Such schedules shall be as short as practicable and will only be considered for inclusion in permits when a discharger has demonstrated the following:

(a) A diligent effort to quantify pollutant levels and the sources of the pollutant in stormwater discharges; and

(b) Documentation of completion of implementation of all technically and economically reasonable control measures.


During periods of heavy rainfall, large pulses of water enter sewerage systems. When these pulses exceed the collection, treatment, or disposal capacity of a sewerage system, overflows occur. This is especially problematic for sewer systems that combine both sanitary sewage and stormwater (Combined Sewer Systems or CSS), such as the City and County of San Francisco's system (discussed under the municipal discharger section). All other municipalities in the region operate two distinct sewer systems. Wet weather is also problematic for separate systems because more water infiltrates the pipes leading to treatment plants. This problem is commonly referred to as inflow/infiltration (I/I). In either case, pulses of water during wet weather may cause untreated or partially treated wastewater to be discharged directly to surface water bodies.

Wet weather overflows of wastewater affect three types of beneficial uses: water contact recreation, non-contact water recreation, and shellfish harvesting. The water quality characteristics that can adversely affect these beneficial uses are pathogens, oxygen-demanding pollutants, suspended and settleable solids, nutrients, toxics, and floatable matter.


On April 11, 1994, the U.S. EPA adopted the Combined Sewer Overflow (CSO) Control Policy (50 FR 18688). This policy establishes a consistent national approach for controlling wet weather discharges from CSS to the nation’s water. The policy requires implementation of nine minimum controls that serve as minimum technology-based requirements pursuant to the Clean Water Act. The policy also requires implementation of a long-term control plan that serves as the water quality-based requirements of the Clean Water Act. The long-term control plan must consider the permittee’s financial capability and provide for the attainment of water quality standards.

The Water Board applies the policy to the City and County of San Francisco’s CSS. San Francisco substantially constructed wet weather control facilities prior to adoption of the CSO Control Policy. Accordingly, since construction was completed in 1997, the Water Board has issued permits to the City and County of San Francisco that require compliance with the provisions of the CSO Control Policy that apply to CSO controls: maintenance of the wet weather facilities to ensure continued maximization of storage and treatment; continued implementation of the nine minimum controls, which constitute the technology-based requirements of the CSO Control Policy; post-construction monitoring to confirm the system’s performance; and re-evaluation of the feasibility of reducing or eliminating discharges to sensitive areas.


In providing protection of waste management units against wet weather overflows, Chapter 15 requires that surface impoundments must have sufficient freeboard to accommodate seasonal precipitation and precipitation conditions specified for each class of waste management unit. Those specified precipitation conditions are probable maximum precipitation for Class I units; and the 1000-year, 24-hour precipitation for Class II units.

To guarantee the protection of water quality, the Water Board will interpret seasonal precipitation to be the 100-year return period wet season for Class I units and the 10-year return period wet season for Class II units. The sources to be used for determining the applicable precipitation for a given return period and location are California Department of Water Resources Bulletin No. 195 (or any update by the Department), local water agency publications, or other sources approved by the Executive Officer.


Cleanup of groundwater pollution sites often includes groundwater extraction, and thus creates the need for proper disposal of treated groundwater. The majority of the groundwater pollution cases in the Region involve surface spills, pipeline breaks, or leakages from tanks, vaults, sumps, surface impoundments, or landfills. Toxic pollutants commonly found in groundwater range from solvents (including volatile organic compounds [VOCs] and semi-volatile organic compounds [SVOCs]), petroleum hydrocarbons, heavy metals, or a combination of these pollutants. In many cases, the treated groundwater is discharged to surface waters via storm drains. These direct discharges would normally require an exception to the prohibitions against discharge into shallow or non-tidal waters.

To address this issue, the Water Board adopted Resolution No. 88-160 (see Chapter 5 Plans and Policies). The Resolution urges dischargers of groundwater extracted from cleanup projects to recycle (reclaim) their effluent. When recycling is not technically and/or economically feasible, discharges must be piped to a publicly-owned treatment works (POTW). Furthermore, as required in State Water Board Resolution 89-21 (see Chapter 5 Plans and Policies), the Water Board recognizes the resource value of the extracted and treated groundwater and urges its utilization for the highest beneficial use for which applicable water quality standards can be achieved.

The Water Board will consider granting an exception to the discharge prohibitions only if (a) it has been demonstrated that neither recycling nor discharge to a POTW is technically or economically feasible, and (b) beneficial uses of the receiving water are not adversely affected. Such an exception is based on the Water Board's recognition that discharges allowed under the exception are an integral part of a program to cleanup polluted groundwater and thereby produce an environmental benefit.

Dischargers shall demonstrate that their groundwater extraction and treatment systems and associated operation, maintenance, and monitoring plans constitute acceptable programs for minimizing the discharge of toxic substances and for complying with effluent limitations deemed necessary for protection of the beneficial uses of receiving waters.

Applications for National Pollutant Discharge Elimination System (NPDES) permits to discharge treated groundwater directly to surface waters will be evaluated on a case-by-case basis. In some cases, the applicant may qualify for the requirements of a general NPDES permit for discharge of treated groundwater. The Water Board has adopted general NPDES permits for the following two types of groundwater cleanup projects:

(a) Groundwater polluted by fuel leaks and other related wastes at service stations and similar sites (NPDES General Waste Discharge Requirements for Discharge or Reuse of Extracted and Treated Groundwater Resulting from the Cleanup of Groundwater Polluted by Fuel Leaks and Other Related Wastes at Service Stations and Similar Sites, NPDES No. CAG912002); and

(b) Groundwater polluted by VOCs (NPDES General Waste Discharge Requirements for Discharge and Reuse of Extracted and Treated Groundwater Resulting from the Cleanup of Groundwater Polluted by Volatile Organic Compounds, NPDES No. CAG912003).

These general permits are intended to streamline a common regulatory process and are not available for groundwater discharges with constituents other than fuels and VOCs. The Water Board may renew, revise, or rescind the permits if deemed appropriate. The general permits specify effulent limitations for discharges to surface water bodies, establish self-monitoring requirements, and identify trigger levels for non-routine constituents that are used to determine if additional effluent sampling and treatability studies are needed. Updates to these two general permits are considered every five years.


Table 4-8 is a list of municipal wastewater treatment facilities (excluding wet weather facilities) within the Region that discharge directly into surface waters. Figure 4-1 shows where these facilities are located in the region. Under normal operational conditions, these POTWs provide a minimum of secondary treatment. In addition, with more than thirty percent of the total flow receives advanced treatment.

Brief discussions of the issues specific to the City and County of San Francisco, South Bay dischargers, the Fairfield-Suisun Sewer District, the Livermore-Amador Valley, and the East Bay Municipal Utilities District are presented below.


The City and County of San Francisco owns and operates the only combined sewer system in the San Francisco Bay Region. In San Francisco’s combined sewer system domestic sewage, industrial wastewater, and stormwater runoff are collected in the same pipes and treated at one of two all-weather secondary treatment plants – the Southeast Water Pollution Control Plant and the Oceanside Water Pollution Control Plant – or at the North Point Wet Weather Facility. The system was designed and constructed with several features intended to minimize combined sewer overflows. First, the system has a peak wet weather treatment capacity significantly in excess of dry weather flows. Second, the system design includes more than 200 million gallons of wet weather storage in large transport/storage (T/S) structures that surround San Francisco. These T/S structures hold back the wet weather flows generated by most storms until they can be routed to the treatment plants. During large storms, wet weather flows consisting mostly of stormwater are discharged through one of thirty-six permitted combined sewer discharge (CSD) outfalls. The T/S structures also include baffles and weirs to hold back solids and floating debris prior to discharge through a CSD outfall.

San Francisco was one of the first municipalities in the nation to complete construction of comprehensive combined sewer overflow controls. This construction program began in 1974 with the publication of the Master Plan Environmental Impact Statement and Report, jointly issued by San Francisco and the U.S. EPA, which described an integrated wastewater control system designed to provide control and treatment for both dry weather sewage and wet weather storm flows, and to achieve long-term average CSD frequencies mandated by the Water Board to protect beneficial uses. The program was fully implemented in 1997 at a cost of approximately $2 billion.


The South Bay municipal dischargers consist of three sewage treatment facilities: the San Jose/Santa Clara Water Pollution Control Plant (WPCP), the Palo Alto Regional Water Quality Control Plant, and the Sunnyvale WPCP. These three plants serve all of the urban communities of Santa Clara County located in the Region. The South Bay municipal dischargers, as shown in Figure 4-1, presently discharge effluent receiving tertiary treatment (secondary plus nitrification, filtration, and disinfection) to shallow sloughs contiguous with the Bay, south of the Dumbarton Bridge.

The existing discharge locations for the Lower South SF Bay municipal wastewater dischargers are contrary to Basin Plan policy concerning discharge prohibitions (listed in Table 4-1). Exceptions to the first three of these prohibitions are discussed in Section 4.2 Discharge Prohibitions Applicable Throughout the Region.

State Water Board Order WQ 90-5 (1990) found that a net environmental benefit exception to these prohibitions could not be made for the three South Bay municipal discharges. However, the Order found that a finding of equivalent protection can be made if water quality based concentration limits for metals and revised mass loading limits for metals are placed in the dischargers' NPDES permits, if Sunnyvale and San Jose/Santa Clara continue avian botulism control programs, and if San Jose/Santa Clara implements mitigation for loss and degradation of endangered species habitat. Order WQ 90-5 also included provisions that would prevent increases in flows that would adversely impact endangered species habitats. In subsequent NPDES permit reissuances and Water Board resolutions from 1993 through 2003, the South Bay municipal dischargers met the three conditions required to support a finding of equivalent protection. The three conditions for granting the discharge prohibition must be confirmed at each NPDES permit reissuance.


The FSSD's tertiary wastewater treatment plant has a dry weather treatment capacity of 17.5 million gallons per day (mgd), a wet weather capacity of 40 mgd, and 45 million gallons of off-line storage capacity. The District is currently treating 13 mgd (1993 dry weather data) from a service population of about 111,000. In order to comply with the Water Board's prohibition against dry weather discharges to the Suisun Marsh, FSSD operates a reclamation project in cooperation with the Solano Irrigation District. However, due to various contractual, legal and economic constraints, only about 40 percent of the treatment plant's annual effluent flow is reclaimed for agricultural irrigation. The remainder is discharged to Boynton Slough in Suisun Marsh.

The Water Board required FSSD to conduct an investigation to evaluate the discharge’s impact on water quality conditions and beneficial uses of the receiving waters. This investigation was completed in 1987 and found that the discharge has some measurable local effects on water quality in Boynton Slough, but that beneficial uses are not impaired by the discharge. The study concluded that, overall and on a year-round basis, the discharge affords a net environmental benefit to Boynton Slough and the Suisun Marsh.

Given the findings of this study, the plant's high degree of operational redundancy and emergency storage capacity, and continued efforts by FSSD to maximize the use of reclaimed water, the Water Board has granted FSSD an exception to the Basin Plan prohibition. The Water Board allows, through the NPDES permit issued to FSSD, that portion of FSSD's tertiary effluent which cannot be reclaimed to be discharged to Boynton Slough on a year-round basis.


The primary Water Board concern in the Livermore-Amador Valley (Valley) is the increase in salt loading that has occurred in the Valley's main groundwater basin. It is projected that with natural saline sources and and historical basin management practices, and with minimal water recycling, there will be a net salt loading increase from an average of 4,000 tons per year to 6,000 tons per year, resulting in a 10 milligram per liter (mg/L) per year increase in total dissolved solids (TDS) in groundwater. As a result, it has become increasingly important to develop and implement an integrated water/wastewater resource operational plan to protect the water quality and beneficial uses of the groundwater basin.

To achieve this goal, the Water Board supports local water management efforts to concurrently improve the salt balance in the main basin, to increase the local water supply, and to reduce the need for wastewater export through recycled water irrigation and groundwater recharge and other basin management practices. SALT MANAGEMENT IN THE LIVERMORE-AMADOR VALLEY

The Livermore-Amador Valley groundwater basin is located in the middle of the Livermore-Amador Valley in eastern Alameda County and is primarily a closed groundwater basin within the Alameda Creek Watershed with multiple groundwater sub-basins of variable water quality. The Main Basin (that portion underlying the Cities of Livermore and Pleasanton) has the highest water quality, supplies most of the municipal wells in the area, and is used to store and distribute high quality imported water.

Alameda Creek and its tributaries recharge the Valley's groundwater basin and serve as channels to convey water released from the South Bay Aqueduct (SBA) to the main basin and the Niles Cone groundwater basin for artificial recharge. During dry weather, creek flow consists primarily of SBA release water.

The Alameda County Flood Control and Water Conservation District, locally known as the Zone 7 Water Agency (Zone 7), is the potable water wholesaler for most of the Valley and operates facilities to import and treat surface water from the State Water Project, groundwater wells, and distribution pipelines. Zone 7 serves as the overall water quality management planning agency for the Livermore-Amador watershed and is responsible for managing the Valley's surface water and groundwater resources for the Valley's drinking water supply.

Dublin-San Ramon Services District (DSRSD) distributes potable water and treats wastewater in the western portion of the Valley, including parts of Contra Costa County. The City of Livermore distributes potable water to about one-fourth of Livermore and treats wastewater from the city and the adjacent national laboratories, Lawrence Livermore and Sandia National Laboratories.

The City of Livermore and DSRSD are member agencies of the Livermore-Amador Valley Water Management Agency (LAVWMA). Since 1980, wastewater has been exported from the Valley via LAVWMA-operated facilities that connect to the East Bay Dischargers Authority's (EBDA) interceptor in San Leandro. These waters are ultimately discharged through the EBDA outfall into south San Francisco Bay west of the Oakland Airport.

The current surface water quality objectives for the Alameda Creek Watershed above Niles (Table 3-7) were adopted in 1975. They were based on historic SBA water quality primarily to prevent degradation by wastewater discharges of imported SBA water being conveyed and used for groundwater recharge during dry weather periods. Wastewater discharges were terminated in 1980. WATER RECYCLING AND VALLEY WATER - WASTEWATER MANAGEMENT

The water and wastewater agencies of the Valley have studied water recycling as an alternative to import of new water supplies and export of wastewater since the early 1970 (see Section 4.16 Water Recycling).

Zone 7, DSRSD and the City of Livermore's interests in water recycling have increased over the years due to droughts, continuing scarcity of new water supplies, institutional barriers to increasing wastewater export capacity from the Valley, and increasing public acceptance of water recycling throughout California. Technological advances and reduced costs of demineralization also now make groundwater recharge with demineralized recycled water a technically viable tool to help manage salt concentrations in the Valley.

Valley-wide water recycling is consistent with the Water Board's policy on recycled water, which states in part that disposal of wastewater to inland, estuarine, or coastal waters is not considered a permanent wastewater disposal solution where the potential exists for conservation and water recycling (see Section 4.16 Water Recycling). As directed by California Water Code (Water Code) Sections 13511 and 13512, the Water Board strongly supports the use of recycled water to supplement existing surface water and groundwater supplies and will work with agencies to facilitate development of water recycling facilities.

The Valley water and wastewater agencies jointly sponsored the "Livermore-Amador Valley Water Recycling Study" (May 1992) that includes a comprehensive investigation of water recycling options. The study documented the Valley's hydrogeology. It also identified and analyzed potential projects throughout the Valley, including irrigation with non-demineralized effluent, groundwater recharge with demineralized effluent, and export of brine. The report included a discussion of how water recycling could be implemented in conformance with Water Board requirements and Zone 7 policies and still manage salt loading on a Valley-wide scale.

The report also detailed a strategy for developing a water recycling program incrementally, beginning with small demonstration projects to gain experience and public acceptance and building up to large-scale projects that could contribute substantially to water supply and wastewater disposal needs in future years.

The 1992 study documented that between 19,000 and 38,000 acre-feet per year of recycled water could be beneficially reused within the Valley via irrigation and groundwater recharge. Well-established technologies and procedures exist for accomplishing such uses and could be in full compliance with Water Board requirements and the Department of Health Services's (DHS) Title 22 CCR requirements. The long-operating Orange County Water District Water Factory 21 project has served as a model for many recycled water groundwater recharge facilities. VALLEY-WIDE SALT MANAGEMENT PLAN

As recommended in the 1992 study, the agencies jointly applied for a Master Water Reuse Permit (Master Permit) to cover proposed water recycling activities throughout the Valley. The Water Board issued the Master Permit in 1993 (Order No. 93-159). The permit specifies the various technical reports that were required to be submitted for review and approval by the Executive Officer before projects could commence operation. In this manner, the Master Permit fully addresses the regulatory requirements that projects must comply with, while facilitating the approval process.

The permit allows small-scale irrigation projects to be developed by the cooperating agencies. Before large-scale recycling projects could be approved, a long-range Valley-wide Salt Management Plan (SMP) was required to be developed and implemented. The Master Permit required further characterization of basin hydrogeology, refinement of salt balance calculations, selection of TDS policy targets and examination of alternative ways to offset natural and recycled sources of salt loadings. The SMP would need to address the water quality objectives for the Alameda Creek Watershed, which state that wastewater disposal/reuse projects be part of an "overall water-wastewater resource operational program developed by the agencies affected and approved by the Water Board."

Zone 7, in partnership with a technical advisory group composed of local water retailers and a Zone 7 citizens committee, prepared the SMP as required by the Master Permit. The development of the SMP occurred through a lengthy public process (1994 to 1999) and resulted in Water Board approval in 2004. Over the years, the scope of the SMP broadened beyond that outlined in the Master Permit to one more resembling a comprehensive watershed and water resources management plan.

The purpose of the SMP is to identify and document the long-term strategy for managing salt and mineral water quality in the Valley’s groundwater basin. The primary strategy is to increase conjunctive use combined with groundwater demineralization in the western portion of the service area to fully offset current and future sources of salt loading to the Valley’s Main Basin. This strategy was designed to also maintain and improve delivered water quality and to facilitate increased use of recycled water using Zone 7 facilities to offset the associated increase in salt loading. Other strategies were identified and may be implemented through Zone 7’s monthly Water Operations Plans using an adaptive management process. GENERAL WATER REUSE PERMIT

The City of Livermore and DSRSD were approved for the General Water Reuse Requirements for Municipal Wastewater and Water Agencies, (General Water Reuse Permit, see Section 4.16 Water Recycling), to administer their current and future recycled water projects involving landscape and/or agricultural irrigation recycling water projects. The General Water Reuse Permit, which delegates the administration of domestic wastewater reuse to water recycling agencies and water agencies, replaces the Master Permit for surface irrigation projects. The General Water Reuse Permit issued to the City of Livermore and DSRSD incorporates the requirements of the approved SMP. The Master Permit will remain on record, and, if needed, will be revised to address any future groundwater recharge projects that may be planned by the two agencies.

Groundwater recharge or conveyance via ephemeral streams is an essential component of the proposed Valley-wide, year-round water recycling and groundwater quality management program. However, projects subject to NPDES requirements are not authorized under the Master Permit. The Master Permit identifies the technical reports necessary to support a future NPDES permit application. The Water Board will consider issuing a separate NPDES permit to the permittees following receipt of a complete NPDES application. WATER BOARD SUPPORT FOR WATER QUALITY MANAGEMENT STRATEGIES PROTECTING THE LIVERMORE-AMADOR VALLEY GROUNDWATER BASINS

The Water Board supports the concept that water recycling is an essential component for planning the Valley's future water supply. Water recycling is particularly important in areas like this, that are dependent on imported water.

As demonstrated by its 2004 approval, the Water Board supports the Salt Management Plan developed by the cooperating agencies in the Valley to facilitate increased use of recycled water to offset salt loading.

The Water Board supports the export of concentrate from the demineralization of groundwater via the LAVWMA and EBDA pipelines when implemented as part of the Salt Management Plan and is protective of beneficial uses of the San Francisco Bay.

The Water Board supports the concept of transport and groundwater recharge through the Valley's ephemeral streams. Recharge of the groundwater basin may be accomplished with imported water, as is done now, or combined with high-quality recycled water under a future groundwater-recharge NPDES permit or WDRs. The year-round, dependable recycled water resource may also be appropriate for streamflow augmentation to enhance beneficial uses of the Valley's ephemeral streams.


The sewer systems of the seven local agencies in the East Bay communities (Alameda, Albany, Berkeley, Emeryville, Oakland, Piedmont, and Stege Sanitary District) have had a serious problem with infiltration/inflow (I/I) during the wet weather season. During major storms, the community's sewers receive up to 20 times more flow than in dry weather. As a result, the communities' sewers overflowed to streets, local watercourses, and the Bay, creating a risk to public health and impairing water. The seven local agencies discharging sanitary sewage deliver sewage to EBMUD's facilities, and thus, EBMUD's interceptors and treatment facilities also subject to overflows during storm events.

The Water Board approved a regional approach -- a combination of community collection system improvements and EBMUD capacity improvements - for correcting wet weather overflows. Following the Basin Plan, EBMUD and the agencies established the following priorities to correct this problem:

  • Substantially reduce or eliminate community sewer overflows with high public health risks;
  • Substantially reduce or eliminate other community sewer overflows; and
  • Eliminate or mitigate interceptor overflows.

In 1985, the East Bay communities completed a multi-year infiltration/inflow (I/I) study, which proposed a $300 million (1985 dollars) comprehensive sewer rehabilitation and relief line program known as the East Bay Infiltration/Inflow Correction Program (ICP), it required 20 years to implement. In a 1986 enforcement order, the Water Board accepted the proposed approach and directed the ICP Program to focus on high public health problems.

In 1986, all agencies submitted Compliance Plans in response to the cease-and-desist orders issued by the Water Board. These plans set forth the design and implementation requirements of each agency's I/I Correction Program.

EBMUD's and the collection system agencies' programs are designed to handle wastewater and I/I flows for up to a 5-year wet weather event. For rainfall events that have a return frequency greater than 5 years, overflows from the sanitary collection and treatment systems may occur. This approach is consistent with the Basin Plan wet weather overflow requirements (Maintenance Level C) adopted for the I/I Correction and the Wet Weather Facilities Program.

The communities have made good progress implementing their ICP eliminating about 60 percent of the high public public health risk overflows. They have also gained a better understanding of how to implement their ICP. This experience has revealed that some of the original planning assumptions underestimated sewer rehabilitation and replacement costs. As a result, the communities revised their programs and the Cities of Alameda, Albany, Berkeley, Oakland, and Piedmont requested extensions to their compliance schedules by 5 to 10 years. In 1993, the Water Board amended its enforcement order giving extensions to some communities' compliance schedules. The amended enforcement order also contains revised compliance reporting requirements.

As part of the regional approach, EBMUD's contribution is a $145 million (1985 dollars) Wet Weather Program, designed to increase treatment capacity to match the communities' flows. The Wet Weather Program includes an expansion of the main wastewater treatment plant, new storage basins, four new remote wet weather treatment plants, new and ungraded pumping stations, and 7.5 miles of new interceptors. This program will increase EBMUD's peak transport and treatment capacity, without which community sewers would continue to overflow. It will also provide treatment for wet weather discharges and meet or exceed Basin Plan requirements.

As of 1995, EBMUD has completed the expansion of the main wastewater treatment plant, all interceptor improvements, construction of the main plant storage basin, and construction of the two principal wet weather treatment facilities (Oakport and Point Isabel). The work remaining includes two pump station improvements, a storage basin, and two wet weather treatment plants. The Wet Weather Program is scheduled for completion in 1998.


This section discusses industrial waste discharges to surface waters under the NPDES program. Other industrial waste disposal practices are discussed in a later section entitled "Hazardous and Nonhazardous Waste Disposal" under Groundwater Protection and Management.

The Water Board has permitted over 320 industrial discharges in the region. They can be separated into two general types: process-related wastewaters and groundwater from cleanup activities. There are about 50 discharges of process wastewater; of these, 15 are classified as major discharges and the rest are mostly small discharges of non-contact cooling water and/or runoff. About 270 of the 320 discharges consist solely of treated groundwater from remediation activities at solvent and/or fuel contamination sites. These are minor in flow relative to the major discharges, and are discussed in more detail in an earlier section entitled "Discharge of Treated Groundwater." Additionally, there are over 1,500 industrial facilities discharging only stormwater runoff. The regulation of these discharges is discussed in a later section entitled: "Urban Runoff Management."

The 15 major discharges are the most significant individual sources of pollutant loadings from industrial discharges. They are identified and described in Table 4-9, and their locations are shown in Figure 4-2. These industries have all installed treatment facilities that can be considered to provide "best available treatment economically achievable" (BAT), and are in compliance with available BAT standards promulgated by the U.S. EPA for each industrial classification.

The Water Board's goal for regulation of industrial discharges is to continue to move beyond treatment technology-based standards to water quality-based standards. With this shift, the industries are challenged to improve existing or develop new treatment and control technologies to achieve higher levels of protection of receiving waters' beneficial uses.

The effect of the Water Board's regulation has been to drastically reduce the pollutant loadings from industrial sources. But with the focus shifting to water quality-based standards, concerns still do exist in certain areas. For example, a major concern is discharge of selenium from oil refineries. Water quality data from the Regional Monitoring Program and other studies will be necessary to identify areas of most concern and help target future pollutant reduction efforts.


The Waste Discharge Permitting Program described in Section 4.12 Industrial Facilities focuses on limiting pollutant discharge to the Bay from industrial and municipal treatment systems. In most situations, however, the overall effectiveness of treatment depends on the type and amount of pollutants that enter these POTWs or industrial treatment system. Some pollutants may cause upset to or interference with the operation of the treatment plant, sludge contamination, or harm to treatment plant workers and the public if discharged into sewer systems. In general, it is often more economical to reduce overall pollutant loading into treatment systems than to install complex and expensive technology at the plant. Both pretreatment and pollution prevention programs are key components of pollutant source control.

The goal of the pretreatment program is to protect treatment plants, worker health and safety, and the environment from the impact of discharges of certain toxic wastes (e.g., explosive and corrosive materials) into collection systems.

The pollution prevention program expands beyond the pretreatment program to include industrial, commercial, and residential sources. The goals of pollution prevention are to:

  1. Reduce or eliminate the discharge of all pollutants that have been found to impact or threaten beneficial uses;
  2. Focus on pollutant source reduction "upstream" of treatment plants, with an emphasis on material recycling, efficient use of chemicals, waste reduction, material and/or product substitution, and process modification; and
  3. Support reduction of pollutant discharges into collection systems through water conservation, recycling, and reuse.

The combined efforts of the pretreatment and pollution prevention programs have influenced thousands of facilities in the Region to significantly reduce the amount of pollutants discharged to the Bay. Between 1986 and 1999, the loading of heavy metals discharged from 27 POTWs with pretreatment programs, were reduced by 59 percent, even though the total volume discharged from these 27 POTWs increased slightly over this period.


Each POTW regulates the types of waste discharged into collection systems leading to its treatment plant. The U.S. EPA, for certain types of waste and industrial categories, sets general standards for discharge to POTWs. Each POTW receiving a large amount of industrial waste and/or with a design flow greater than 5 million gallons per day (MGD) is required to develop and implement a pretreatment program, including enforce its own local discharge limits. The goal is to both protect treatment plants and ensure that the POTW is in compliance with its own discharge permit.

The Water Board oversees the implementation of the California pretreatment program under the California Water Code and federal Clean Water Act, although U.S. EPA retains its oversight role and is still actively involved in inspections and enforcement activities. POTW pretreatment programs must include components as specified in federal regulations and program descriptions incorporated into the NPDES permit for each POTW.

Specific monitoring and reporting requirements for the 27 POTWs in the Region with approved pretreatment programs are contained in the NPDES Permits for the POTWs. Major budgeted program tasks for the Water Board's oversight activities include pretreatment compliance inspections and audits; annual and semiannual report reviews; program modifications, particularly local limits revisions; and enforcement activities.


The Water Board supports reducing toxic discharges through pollution prevention and expansion of the pretreatment program. This general approach to minimizing waste discharge is a necessary element in the implementation of the State Water Board's Mass Emission Strategy and will become increasingly important as alternative uses of wastewater are developed.

The Water Board's pollution prevention program is a two-tiered program that consists of a general and a targeted program. The first tier is a general program, requiring dischargers to focus on long-term pollution prevention and overall reduction of toxics entering collection systems. The general program is structured to allow dischargers to develop and direct pollution prevention efforts in its own service area. It also allows dischargers to reduce toxic pollutant loading to their plants and remain in compliance with their discharge permit.

The second tier is a targeted program aimed to ameliorate existing water quality problems. The goal of targeted programs is to reduce the total amount of a specific pollutant (or pollutants) discharged to specific water bodies. Targeted programs are required when numeric or narrative water quality objectives are exceeded and beneficial uses are impaired or threatened.

Both the general and targeted pollution prevention programs will take multimedia concerns into account by coordinating with other relevant regulatory programs related to air and land disposal (e.g., sludge or biosolids).

All POTWs with an approved pretreatment program and all major industrial dischargers are required to develop and implement a general pollution prevention program within their jurisdiction. Dischargers are required to develop and implement a targeted program under the circumstances described in Section Targeted Pollution Prevention for POTWs.

Presently, dischargers with required pollution prevention programs submit mid-year progress reports and/or a comprehensive annual report, which discusses progress and accomplishments along with program changes, and future program goals, developments and effectiveness measures. With forthcoming data needs for watershed permits, reporting formats will be standardized to improve comparability between programs. GENERAL POLLUTION PREVENTION PRIORITIES

The following are the Water Board’s priorities for the pollution prevention program in the coming years:

  1. Encourage continued region-wide leadership across all pollution prevention programs through cross-program and cross media coordination, watershed based problem solving, and adaptability to new concerns through collaboration and partnerships.
  2. Develop strategies to measure effectiveness of pollution prevention efforts over the long and short term.
  3. Recognize and promote excellence through pollution prevention awards to programs that demonstrate resourcefulness, effectiveness, innovation, wide outreach (business, residential, and educational), and that take action to promote region-wide solutions. POLLUTION PREVENTION PROGRAM HISTORY

In 1988, the Water Board began requiring “source control” programs from the three South Bay POTWs. In 1992, the Water Board required the remaining POTWs with pretreatment programs to develop and implement Waste Minimization Programs. Specifically, this included targeted programs for POTWs to reduce pollutants that exceeded water quality criteria, general programs for the remaining POTWs, and waste minimization audits for select industrial facilities discharging directly to surface waters. In 1993, the “Waste Minimization Program” was changed to “Pollution Prevention Program.”

The Water Board formed the Bay Area Pollution Prevention Group (BAPPG) in 1990 and continues to support its significant successes in reducing pollution through product and chemical bans, targeted initiatives to reduce heavy metals, and regional technology transfer, outreach, and resource sharing.

In 2000, the state legislature enacted Water Code Section 13263.3 on pollution prevention programs. Also in 2000, the Policy for Implementation of Toxic Standards from Inland Surface Waters, Enclosed Bays and Estuaries of California (State Implementation Plan, or SIP) became effective, which addresses pollutant minimization programs.

In 2003, the Water Board adopted Resolution No. R2-2003-0096 promoting collaboration between the Bay Area Clean Water Agencies (BACWA) and the Water Board. It established 11 guiding principles for developing tools and guidance for POTW pollution prevention programs to balance program flexibility and program effectiveness. The products developed from this effort include a guidance document for pollution prevention program managers seeking to improve outreach and effectiveness of their programs, “Pollution Prevention Guidance and Tools for POTWs” (April 2005). GENERAL POLLUTION PREVENTION PROGRAMS FOR POTWs

The general program is designed to allow individual POTWs to develop and direct long-term pollution prevention efforts according to local needs and is more flexible than targeted programs. General programs should contain the following elements:

  1. Pretreatment program review and enhancement should include a general review of opportunities for incorporating waste reduction goals into inspections, enforcement, and permitting (such as increased inspection, improved process flow measurements, etc.) In addition, previously unregulated types of industrial and commercial facilities that discharge pollutants of concern to the POTW should be identified. Each general program should include provisions for two additional categories of discharge that are not covered under the federal regulations (such as waste oil disposal, household products, car and truck washing operations, medical and dental facilities, etc.).
  2. Prioritize the need for and conduct audits of industrial users. The criteria for prioritization should include discharge of pollutants of concern, volume of flow, industrial user compliance, and opportunities for waste reduction.
  3. Periodic analysis of the waste discharge to determine which pollutants are currently problems and/or which pollutants may pose problems in the future.
  4. Identify sources of all pollutants of concern.
  5. Identify and implement tasks to reduce the sources of pollutants of concern.
  6. Design and conduct public education programs aimed at changing public behavior through educating the public about a pollutant, its sources, its impact to beneficial uses, how it is released into the environment, and where appropriate, options for safer product use, substitution, and product disposal (e.g., household hazardous waste management). Such efforts include advertising outreach and household hazardous waste programs. Current regional successes include product bans and advertising campaigns in English, Spanish, and Chinese. Successful outreach results in changing behaviors that lead to changes in purchasing behavior, or the way a toxic product is used, recycled, or disposed.
  7. Coordination with other programs involving recycling, reuse, and source reduction of toxic chemicals. This includes programs involving other media, such as air, hazardous waste, and land disposal. This might include developing programs for joint inspections and sharing in enforcement activities.
  8. An effectiveness monitoring program specifically designed to measure the success or effectiveness of specific pollution prevention activities, as well as overall successes achieved in reducing toxic loads to the receiving watershed where possible, as well as to air, or land via sludge disposal. Such evaluations of program effectiveness are conducted on a regular basis. TARGETED POLLUTION PREVENTION PROGRAMS FOR POTWs

The purpose of targeted pollution prevention programs is to reduce the total amount of specific toxic pollutants being discharged to POTWs. Targeted programs are more intensive versions of the general programs and are focused only on one or a select number of pollutants.

Specifically, targeted programs are required for POTWs when any of the following conditions exist:

  1. When numeric or narrative water quality objectives are exceeded and beneficial uses are impaired or threatened;
  2. Are required as part of a TMDL or site specific objective (SSO) implementation plan;
  3. Are required under the SIP when there are effluent limit compliance problems; or
  4. As authorized under the Water Code Section 13263.3.

The Water Board may, at its discretion, require dischargers to implement pollution prevention plans consistent with Water Code Section 13263.3 and the SIP.

In those areas of a watershed or the Estuary identified as exceding water quality objectives or having impaired beneficial uses, dischargers that are significant contributors to the water quality problem will be identified and will be required to participate in a targeted waste minimization (pollution prevention) program. In addition to general program elements, a targeted pollution prevention program involves quantifying the sources to the POTW of the targeted pollutants in question. It may also be necessary to conduct further monitoring of the targeted pollutants in the receiving water, sediment, and biota by identified dischargers to POTW systems and/or POTWs at and near their discharge locations in order to more precisely determine associated effects.

A targeted program must also initiate reductions in pollutant loading through a control strategy designed to achieve the goal of maintaining concentrations of reportable priority pollutants in the effluent at or below the effluent limit, focusing on the most effective and economic control measures first. These reductions may be achievable through focused public outreach, implementation of Best Management Practices (BMPs), technical information transfer regarding effective management techniques, or installation of appropriate technologies.

The targeted program shall include all elements of the general program, expanding where appropriate to maximize the reduction of the targeted pollutants.

Targeted programs may also require other options such as performance-based effluent concentration limits and mass limitations for the pollutants of concern, in order to attain water quality objectives in the receiving water body. DIRECT INDUSTRIAL DISCHARGER POLLUTION PREVENTION PROGRAM

Industrial entities discharging directly to receiving waters instead of public sewer systems are also subject to similar pollution prevention requirements. Overall source reduction and recycling of hazardous wastes, including audits, planning, and reporting to the Department of Toxic Substance Control (DTSC) is required under the Hazardous Waste Source Reduction and Management Review Act of 1989 (Title 23, CCR, Ch 31). Rather than require separate pollution prevention programs, major dischargers were asked to submit copies of the required pollution prevention reports (those sections specifically addressing liquid waste and reduction of pollutants discharged to water) to the Water Board. These dischargers submitted initial plans for pollution prevention, including detailed descriptions of tasks and schedules, in 1992.

In the event that existing pollution prevention reports do not adequately address reduction of toxic pollutants in effluent, the Water Board will require additional information.

In cases where water quality problems exist or where beneficial uses are impaired or threatened by direct industrial dischargers, focused pollution prevention programs similar to POTW targeted programs will also be required. In cases where Water Board staff determines that independent audits, as opposed to audits conducted by the involved companies, the issue will be brought before the Water Board. The effort should result in the reduction or elimination of specific pollutants of concern.


During periods of rain, water flushes sediment and pollutants from urbanized parts of the Estuary (Figure 4-3) into storm drain systems. These drains discharge directly to surface waters within the region, except in San Francisco where stormwater is mixed with sewage and directed to the treatment plant.

Urban runoff contributes significant quantities of total suspended solids, heavy metals, petroleum hydrocarbons, and other pollutants to the waters of the region. The impacts of pollutants in urban runoff on aquatic systems are many and varied. For example, small soil particles washed into streams can smother spawning grounds and marsh habitat. Lead and petroleum hydrocarbons washed off from roadways and parking lots may cause toxic responses in aquatic life and exemplify another kind of threat. The US EPA found levels of cadmium, copper, lead, and zinc in urban runoff exceeded freshwater acute aquatic life criteria in 9 to 50 percent of samples taken across the country. The chronic criteria for these metals, beryllium, cyanide, mercury, and silver were exceeded in at least 10 percent of the samples. In the San Francisco Bay Region, the Association of Bay Area Governments (ABAG) has found consistently high levels of hydrocarbons in urban runoff.

The Water Board's urban runoff management program focuses on reducing pollutant transport through stormwater drain systems into surface waters. In general, measures that will effectively limit storm drain pollutant discharge will also limit direct runoff of pollutants into creeks, streams, and lakes.

The program is structured around the municipalities and local agencies responsible for maintaining storm drain systems, and three classes of activities that are responsible for significant amounts of pollutant influx to those public storm drain systems: highways under the jurisdiction of the California Department of Transportation (Caltrans), industrial activities, and construction on areas larger than 5 acres.

Within each of these program areas, the Water Board's urban runoff management approach emphasizes general, long-term planning to avoid any increases in pollutant loading, and more structured, intensive approaches when existing water quality problems require immediate action.

A large part of the Water Board's work in managing urban runoff involves supporting local planning and investigation. The program includes:

  • Organizing local ad hoc task forces within each hydrologic sub-region (see maps in Chapter 2) to facilitate investigations and design of appropriate control strategies. These task forces include representatives from local government, point source dischargers, local industries, the Water Board, and U.S. EPA.
  • Developing cooperative investigation and control strategies utilizing the expertise and resources of point source dischargers in each of the receiving water segments.
  • Supporting research by the San Francisco Estuary Institute, ABAG, U.S. EPA, and others entities to better define the impacts of urban runoff discharges.
  • Participating on the State Water Board Stormwater Quality Task Force and the development and implementation of a statewide urban stormwater best management practices manual.
  • Working with other agencies such as the Bay Area Air Quality Management District and the Metropolitan Transportation Commission to ensure that transportation related strategies and plans will reduce the impact on receiving waters from transportation system runoff discharges.


The Water Board's strategy for managing pollutants and sediment in urban runoff entering and being discharged public storm drain systems is two-tiered. All cities and counties are encouraged to develop and implement voluntary programs aimed at pollution prevention throughout the region (Baseline Control Program). Selected cites and counties, by virtue of the amount of pollutants being discharged from their storm drain system, impact of those discharges on receiving waters, or population, are required to develop pollution prevention programs and take steps to reduce runoff into drain systems (Comprehensive Control Program).

The first major step in addressing pollutant loading to public storm drains was to compile basic information on existing systems. A Board survey of local agencies owning or responsible for storm drain systems and flood control agencies had limited and often dated information on the storm drain systems that they own or manage. In addition, flow and water quality data for storm drain system discharge were virtually nonexistent. The survey also found that current management of storm drain systems is primarily focused on flood control, with storm drainage inlets, lines, and catch basins scheduled for cleaning annually or on an as-needed basis for flood prevention purposes. BASELINE CONTROL PROGRAM

All local agencies, including special districts, in the cities and counties in the region (see Table 4-10) that own or have maintenance responsibility for storm drain systems should develop and implement a baseline control program.

The goal of the baseline control programs is to prevent any increase in pollutants entering these systems. To a large extent, this goal can be achieved by including consideration of pollutant runoff into storm drain systems in the course of local planning efforts and encouraging "good practice" techniques.

Components of baseline control programs should include: review and update of operation and maintenance programs for storm drain systems; development and adoption of ordinances or other planning procedures (such as CEQA review) to avoid and control pollutant and sediment loading to runoff as part of the normal design and construction of new and significant redevelopment (both during construction and after construction is completed); and education measures to inform the public, commercial entities, and industries on the proper use and disposal of materials and waste and correct practices of urban runoff control. Baseline control programs should also include surveillance, monitoring, and enforcement activities to ensure and document implementation.

Similarly, flood control agencies should consider the impact of their projects on receiving waters. Flood management projects, facilities, or operations should be designed, operated, and maintained to reduce the amount of pollutants in stormwater discharges as well as achieving flood control objectives.

The Water Board will support and encourage the development and implementation of baseline control programs in cooperation with cities and counties. Board staff may provide technical guidance and support, facilitate ad-hoc working groups including people with expertise and experience in POTW pollution prevention programs and local hazardous waste management, and participate in development of model ordinances.

The programs should be coordinated with POTW and industrial pollution prevention programs and local hazardous materials management programs.

In addition, the Water Board will focus its surveillance, monitoring, and enforcement activities on and review Environmental Impact Reports on new development and significant redevelopment and focus its surveillance, monitoring, and enforcement activities to support implementation of effective baseline control programs. The effectiveness of a municipality's baseline control program will also be considered when issuing NPDES permits for construction activities pursuant to the Water Board's Construction Activity Control Program.

The Water Board requires the local agencies, special districts, and municipalities listed in Table 4-10 to submit annual reports (pursuant to Section 13225(c) of the California Water Code) describing their baseline control programs. These reports are due on September 1 of each year and should describe:

  • Operation and maintenance activities associated with the storm drain system;
  • Master planning procedures and documentation of activities associated with control;
  • A list of all new development and significant redevelopment projects with documentation that urban runoff control measures have been required and are being implemented;
  • Documentation of educational measures;
  • Documentation of surveillance, monitoring, and enforcement activities; and
  • A qualitative evaluation of program effectiveness, including, but not limited to, program accomplishments, funds expended, staff hours utilized, an overall evaluation, and plans for the upcoming year.

To the extent that voluntary implementation of baseline control programs is not realized, the Water Board will act, where necessary, to require individual local agencies to investigate specific runoff discharges, quantify pollutant loads, and identify and implement control strategies for pollutant runoff into storm drains. Where necessary, require individual local agencies to file a Report of Waste Discharge or NPDES permit application for the implementation of baseline control programs.

Cities and counties should review and revise their planning procedures and develop or revise comprehensive master plans to assure that increases in pollutant loading associated with newly developed and significantly redeveloped areas are, to the maximum extent practicable, limited. Areas that are in the process of development, or redevelopment offer the greatest potential for utilizing the full range of structural and non-structural control measures to limit increases in pollutant loads. Comprehensive planning must be used to incorporate these measures in the process of developing. Cities and counties should fully utilize their authority under CEQA to assure implementation of control measures at all proposed development and significant redevelopment projects. COMPREHENSIVE CONTROL PROGRAM

The goal of the Water Board's comprehensive control program is to remediate existing water quality problems and prevent new problems associated with urban runoff. To achieve this, the program focuses on reducing current levels of pollutant loading to storm drains to the maximum extent practicable. The Water Board's comprehensive program is designed to be consistent with federal regulations (40 CFR 122-124) and is implemented by issuing NPDES permits to owners and operators of large storm drain systems and systems discharging significant amounts of pollutants. The conditions of each NPDES stormwater permit require that entities responsible for the systems develop and implement comprehensive control programs.

The regulations authorize the issuance of system-wide or jurisdiction-wide permits and they effectively prohibit non-stormwater discharges to storm drains. They also require listed municipalities to implement control measures to reduce pollutants in urban stormwater runoff discharges to the maximum extent practicable. The Water Board will, where necessary, require stormwater discharge permits for discharges not cited in the regulations which are a significant contributor of pollutants to waters of the region.

The comprehensive urban runoff control program includes all elements of the baseline control program designed to prevent increases in pollutant loading. To reduce current pollutant loading to the maximum extent practicable, the program also includes:

  • Characterization of urban runoff discharges to the extent necessary to support program development;
  • Elimination of illicit connections and illegal dumping into storm drains;
  • Development and implementation of measures to reduce pollutant runoff associated with the application of pesticides, herbicides, and fertilizer;
  • Development and implementation of measures to operate and maintain public highways in a manner that reduces pollutants in runoff; and
  • Effective pollution reduction measures may include educational activities such as painting signs on storm drain inlets and regulation of activities such as application of pesticides in public right-of-ways.

Each NPDES stormwater permit issued by the Water Board will require an annual report evaluating the effectiveness of its comprehensive urban runoff control program. At a minimum, quantitative monitoring, a detailed accounting of program accomplishments (including funds expended and staff hours utilized), an overall evaluation of the program, and plans and schedules for the upcoming year shall be used to assess effectiveness.

The Water Board's urban runoff control program is still relatively new. Table 4-10 lists the entities in each area that have implemented comprehensive control programs. In addition, there is a need to develop and implement similar programs in the urban and rapidly developing areas of Solano County and the cities of San Rafael, Novato, Petaluma, Napa, and Benicia, and the Ports of Oakland, Richmond, and San Francisco. Urban runoff discharges from these areas are considered significant sources of pollutants to waters of the region and may be causing or threatening to cause violation of water quality objectives. The Water Board intends to consider similar action for these at a later time. The City and County of San Francisco is not permitted under the storm water program because it has a combined (sanitary and storm) sewer system operating in accordance with existing NPDES permits.

The Water Board will conduct surveillance activities and provide overall direction to verify and oversee implementation of urban runoff control programs. Technical guidance for prevention activities, the identification, assignment, and implementation of control measures, and monitoring will be developed.


An essential component of reducing pollutant loading to storm drain systems involves managing runoff from public roads. While many roads fall under the jurisdiction of entities responsible for storm drain systems, public highways are controlled by the California Department of Transportation (Caltrans). In order to ensure that all public highways are maintained to reduce pollutant runoff, the Water Board issued a stormwater NPDES permit to Caltrans in August, 1994. The permit requires implementation of a highway Stormwater Management Plan which addresses the design, construction, and maintenance of highway facilities relative to reducing pollutant runoff discharges to the maximum extent practicable.

The highway runoff management plan shall include litter control, management of pesticide/herbicide use, reducing direct discharges, reducing runoff velocity, grassed channels, curb elimination, catch basin maintenance, appropriate street cleaning, establishing and maintaining vegetation, infiltration practices, and detention/retention practices. In addition, the plan must include monitoring the effectiveness of control measures, runoff water quality, and pollutant loads. When possible, Caltrans is expected to coordinate with existing agencies and programs related to the reduction of pollutants in highway runoff.


Industrial stormwater sources are subject to best available technology (BAT) economically-based standards. Federal regulations require stormwater permits for any site where industrial activity takes place (or has in the past), and materials are exposed to stormwater. The definitions of industrial activities subject to these permits (provisions of Title 40 Code of Federal Regulation, Part 122.26, revised December 18, 1992) are incorporated by reference into this plan. This incorporation by reference is prospective including future changes as they take effect. The Water Board will require an NPDES permit for the discharge of stormwater from all industrial facilities where such activities occur. These permits apply to the discharge from any system used to collect and convey stormwater at industrial sites. These sites include, but are not limited to, industrial plant yards, access roads and rail lines, material and refuse handling areas, storage areas (including tank farms) and areas where significant amounts of materials remain from past activity. Permits are issued both to privately and publicly (federal, state, and municipal) owned facilities.

The Water Board's permitting strategy for industrial facilities is based on a four-tier set of priorities for issuing permits. At a minimum, all permits will require compliance with all local agency requirements. General permits for industrial facilities will not be less stringent than individual permits. TIER I: GENERAL PERMITTING

The majority of stormwater discharges associated with industrial activity in the region will be covered under a general permit issued by the State Water Board in November, 1991. TIER II: SPECIFIC WATERSHED PERMITTING

In some watersheds, water quality has been impacted by stormwater discharges from facilities associated with industrial activity. Facilities within these watersheds will be targeted for individual stormwater permits or regulation under watershed-specific general permits. The Water Board issued a general permit for industrial activity in the portion of Santa Clara County that drains to South San Francisco Bay to support the county's comprehensive control program and will consider a similar general permit for Alameda County at a later time. TIER III: INDUSTRY-SPECIFIC PERMITTING

Specific industrial categories will be targeted for individual or industry-specific general permits. For example, the Water Board issued a general permit for storm water discharges from boatyards in August 1992. The use of general permits is intended to alleviate the administrative burden of issuing storm water permit for individual industrial facilities. In some cases, such as large U.S. Department of Defense facilities, individual sites or classes of sites may be significant sources of pollutants, and individual permit(s) specific to these classes of sites are warranted.

The Water Board considers stormwater discharges from automotive operations, including gas stations, auto repair shops, auto body shops, dealerships, and mobile fleet-washing businesses to be significant sources of pollutants to waters in the region. Local agencies implementing comprehensive control programs are addressing these discharges through ordinances as part of their comprehensive control programs. The effectiveness of local measures will be assessed before the Water Board considers permitting these under a separate industrial permit. TIER IV: FACILITY-SPECIFIC PERMITTING

A variety of factors will be used to target specific facilities for individual permits, such as amount and characteristics of runoff, size of facility, and contribution to existing water quality problems. Permitted individual facilities will be required to identify "hot areas" where runoff may contact pollutants; activities that may release pollutants to runoff; segregate stormwater discharges from the "hot areas;" and identify and implement control measures for "hot areas.” In addition, permittees will be required to eliminate all non-stormwater discharges to storm drain systems unless authorized by an NPDES permit or determined not to be a source of pollutants requiring an NPDES permit.


The Water Board will require an NPDES permit for the discharge of stormwater from construction activities involving disturbance of five acres or greater total land area or are part of a larger common plan of development that disturbs greater than five acres of total land area. The majority of construction activity discharges in the region will be permitted under a general permit issued by the State Water Board in 1992. Permit conditions address pollutant and waste discharges occurring during construction activities and the discharge of pollutants in runoff after construction is completed. Permit conditions are consistent with the Water Board's erosion and sediment control policy (Resolution No. 80-5) and consistent with local agency ordinance and regulatory programs. The intent of the permit is not to supersede local programs, but rather to complement local requirements. This will require local agencies to effectively address construction activities through their early planning, CEQA processes, and implementation of development control measures as part of their baseline or comprehensive control programs.


Agricultural wastewaters and the effect of agricultural operations must be considered in terms of land use practices and controls developed in the agricultural element of land use plans. The activities of primary importance to water quality in this basin are animal confinement and irrigation practices. Agricultural pesticide use and limits on fertilizer application are not specifically considered because of the limited applicability in this region.


Animal confinement operations such as kennels, horse stables, poultry ranches, and dairies, raise or shelter animals in high densities. Wastes from such facilities can contain significant amounts of pathogens, oxygen-depleting organic matter, nitrogen compounds, and other suspended and dissolved solids. In addition, erosion is also a common problem associated with these facilities. Runoff of storm or wash water can carry waste and sediment and degrade receiving surface waters. Groundwaters can also be degraded when water containing these wastes percolates into aquifers. The risk of water quality degradation increases during the rainy season when animal waste containment and treatment ponds are often overloaded.

Minimum design and management standards for the protection of water quality from confined animal operations are promulgated in Title 23, California Code of Regulations, Chapter 15, Article 6. These regulations prohibit the discharge of facility wash water, animal wastes, and stormwater runoff from animal confinement areas into waters of the state. They also specify minimum design and waste management standards including:

  • Collection of all wastewaters;
  • Retention of water within manured areas during a 25-year, 24 hour storm;
  • Use of paving or impermeable soils in manure storage areas; and
  • Application of manures and wastewaters on land at reasonable rates.

The Water Board has the authority to enforce these regulations through Waste Discharge Requirements.

Facilities such as the dairies located in Marin and Sonoma counties and horse boarding stables are typical of animal confinement operations within the region. DAIRY WASTE MANAGEMENT

Much of the land within the Tomales Bay, Petaluma River, Napa, and Sonoma Valley watersheds is used for agricultural purposes. Within these watersheds, a significant number of livestock are housed and grazed.

Animal waste can cause water quality problems through runoff into surface and groundwaters of the state. Stockpiled manure, washwater, and stormwater runoff from corrals, pens, and other animal confinement areas are potential sources of water pollution due to their high bacteria levels (the coliform group used as indicators), ammonia, nitrate and suspended solids. Detergents, disinfectants, and other biocides commonly used may also contribute to the toxicity of animal wastes. These constituents can be extremely deleterious to fish and other forms of aquatic life. High bacterial levels have had an adverse impact on shellfish resources in the region (i.e., commercial shellfish harvesting in Tomales Bay).

Problems facing the dairy industry include manure containment during the rainy season, appropriate manure dispersal on pasture land, and implementation of range management practices aimed at water quality protection. The availability of ample farm and pastureland is therefore extremely important in managing animal waste.

Since the 1970s, the cooperative relationship between the Water Board and the dairy industry has been an important aspect of dairy waste control. That relationship has been instrumental in the construction of dairy waste handling, treatment, and disposal facilities in the late 1970s. However, proper waste control management is just as important as the physical facility. Management techniques include routing wash water and drainage to impervious holding and storage areas, constructing manure storage areas controlling both subsurface infiltration and runoff, stormwater overflow protection for retention basins, and applying manures and wastewater on land at reasonable rates for maximum plant uptake of nitrogen.

Poor practices that have led to water quality problems in the past include: inadequate maintenance and operation of facilities; overloading treatment and storage facilities; increase of herd size without commensurate additions to waste handling facilities; poor range management practices; and simple neglect of seasonal waste management responsibilities. DAIRY WASTE REGULATION

Both the regulation and the support services for the dairy industry involve several federal, state, and local agencies. Each has its particular role and mission, but all share the goal of protecting the beneficial uses of state waters while assisting dairies in complying with regulations while conducting their day-to-day business. The following agencies play a direct role in dairy waste management and regulation:

  • California Regional Water Quality Control Board
  • California Department of Fish and Game
  • Agricultural Stabilization and Conservation Services
  • U.S. Department of Agriculture — Soil Conservation Service
  • University of California Cooperative Extension Farm Advisor
  • County Farm Bureaus
  • Resource Conservation Districts

To address dairy waste management concerns, dairy operators in Marin and Sonoma Counties have formed a Dairy Waste Committee. The Dairy Waste Committee supports dairy operators in their efforts to solve waste control problems and locate technical and financial assistance. The Committee serves as a vehicle through which the Water Boards and California Department of Fish and Game can disseminate information on water quality regulations and requirements. This committee does and will continue to play an important role in any successful waste control program.

Additionally, the Southern Sonoma and Marin County Resource Conservation Districts (RCDs) have a cooperative, voluntary program in which a farmer agrees to use the land within its capabilities, develop a conservation plan, and apply conservation practices to meet objectives and technical standards of the RCDs. In turn, the RCD agrees to furnish the farmer with information and technical assistance in order to carry out the conservation plan.


Generally, discharges are subject to Waste Discharge Requirements (WDRs) issued by the Water Board. However, the Water Board may waive WDRs where such a waiver is not against the public interest and still assures the protection of beneficial uses of state waters. For the present, the Water Board has been waiving WDRs for dairies where proper waste control facilities are in place and management practices are in conformance with the California Code of Regulations - Title 23, Article 3, Chapter 15 (Discharge of Waste to Land).


In 1990, the State Water Board established a Dairy Waste Task Force to look at the dairy industry statewide and develop standards for dairy regulation. The main emphasis has been on developing better communication and guidance materials for the industry; developing a dairy survey form to help the Water Boards determine if a dairy qualifies for a waiver from WDRs; determining the number and location of dairies; develop more uniform WDRs; and preparing an outreach program aimed at the dairy industry, local government, and the public.

The Water Board directs the Executive Officer to continue the following staff activities:

  • Work with the dairy industry through the local dairy waste committees, County Farm Bureaus, RCDs, and other local/state agencies in obtaining cooperative correction of dairy waste problems.
  • Recommend adoption of WDRs in those cases where water quality objectives for waters within an agricultural watershed are consistently exceeded, or where corrective action is unsuccessful in eliminating either the short- or long-term water quality problems or threats. The Water Board may choose to take enforcement action through the issuance of a Clean-up and Abatement Order or assess monetary penalties in those cases where dairy practices have resulted in or threaten to cause a condition of pollution or nuisance in surface waters through the issuance of Administrative Civil Liability or referral to the California Attorney General's Office.
  • Monitor the compliance of dairy waste management programs with regional goals and implement the recommendations of the State Dairy Waste Task Force.


An increase in the concentration of soluble salts contained in percolating irrigation water is an unavoidable result of consumptive use of water. Salt management within soils and groundwater is considered separate from water management, but is closely related to drainage control and wastewater operations. For irrigated agriculture to continue in the future, acceptable levels of salts in soils and groundwaters must be controlled.

Maintenance of a favorable salt balance, that being a reasonable balance between the import and export of salts from individual basins, must be considered to control increases in mineral content. This is especially applicable for the Livermore and Santa Clara Valley groundwater basins.

The ultimate consequences of regulatory action for irrigation operations must be carefully assessed. The "no-degradation" concept in connection with salt levels is not appropriate in all circumstances.

A concept of minimal degradation might be considered in some areas. It would need to be coupled with management of the surface and underground water supplies in order to assure acceptable degradation effects. If minimal degradation is considered, it can be offset by either recharge and replenishment of groundwater basins with higher quality water that will furnish dilution to the added salts, or by drainage of degraded waters at a sufficient rate to maintain low salts and salts leaving the basin. To aid recharge and dilution operations, additional winter runoff can be stored in surface reservoirs for subsequent use with either surface stream or groundwater basin quantity/quality management.


Per Water Code Section 13050, recycled water means water which, as a result of treatment of waste, is suitable for a direct beneficial use or a controlled use that would not otherwise occur and is therefore considered a valuable resource. To date in this Region, disposal of most municipal and industrial wastewater has primarily involved discharges into the Region's watersheds and the Estuary. With growing awareness of the impacts of toxic discharges, drought, future urbanization, and growth on the local aquatic habitat, there is an increasing need to look for other sources of water. Increasingly, conservation and water recycling (formerly referred to as reclamation) will be needed to deal with these long-term water issues. The Water Board recognizes that people of the Region are interested in developing the capacity to conserve and recycle water to supplement existing water supplies, meet future water requirements, and restore the Region's watersheds and Estuary. Disposal of wastewater to inland, estuarine or coastal waters is not considered a permanent solution where the potential exists for conservation, water recycling, and reuse.

The Constitution of California, Article X, declares that, "...because of the conditions prevailing in the state, the general welfare requires that the water resources of the state be put to beneficial use to the fullest extent to which they are capable, and that the waste or unreasonable use or unreasonable method of use of water be prevented, and that the conservation of such waters is to be exercised with a view to the reasonable and beneficial use thereof in the interest of the people and for the public welfare." In other words, when suitable recycled water is available, it should be used to supplement existing water supplies used for agricultural, industrial, municipal, and environmental purposes.

The Water Board also recognizes and supports the concept that water reuse is an essential component for planning future water supply, especially in areas dependent on imported water. This includes projects that use recycled water to increase the local water supply, to improve the salt balance in the groundwater basin, or to reduce the need for wastewater export through recycled water irrigation and groundwater recharge with imported water or with high-quality recycled water. The year-round, dependable recycled water resource may also be appropriate for stream flow augmentation to enhance beneficial uses of streams.

State Water Board Resolution 77-1, adopted in 1977, requires the State and Regional Water Boards to encourage water recycling projects for beneficial use using wastewaters that would otherwise be discharged to marine or brackish receiving waters or evaporation ponds. The resolution also specifies using recycled water to replace or supplement the use of fresh water or better quality water, and to preserve, restore, or enhance in-stream beneficial uses, including fish, wildlife, recreation and aesthetics associated with any surface water or wetlands.


Before a wastewater producer can obtain an increase in connections and discharge flows under the Water Board's NPDES program, it must demonstrate that a maximum effort has been made to develop and implement a credible and effective water recycling program. This program must be integrated with a source control program (Pretreatment and Pollution Prevention Program (Section 4.13 Pretreatment and Pollution Prevention)) and a water conservation program.

All water recycling projects involve three components: 1) treatment of wastewater to produce water of quality suitable for the intended reuse; 2) distribution, which may also include storage, to convey the treated water to the place(s) of use; and 3) the end use, reuse. The most common types of reuse involve discharges to land for irrigation of landscape plants or crops, but reuse may also include non-discharge uses such as for cooling water or toilet flushing. Each of these components is subject to various design and operational requirements specified in the Water Recycling Criteria (WRC) codified at Title 22, CCR, Division 4, Chapter 3, which were extensively revised and updated by Department of Health Services (DHS) from 1993 to 2001.

The Water Board in conjunction with DHS implements the WRC. DHS and the State Water Board have entered into a Memorandum of Agreement (MOA) on Use of Reclaimed Water. The intent of the MOA is to insure that there is coordination among DHS, the State Water Board and the Regional Water Boards to implement the recycled water program.

The Water Board is the permitting agency for water recycling projects through issuance of water recycling requirements, also called Water Reuse Requirements (WRRs). The WRRs require a discharger proposing a new water-recycling project to prepare an engineering report describing the project, for review and approval by DHS. The Water Board may then prescribe WRRs for the project based on recommendations from DHS. WRRs include relevant specifications from the WRC and other applicable requirements based on Water Board plans and policies, such as effluent limits and operation, and monitoring and reporting requirements. WRRs may be issued for discrete single-facility reuse projects or for large-scale projects such as municipality-based reuse programs involving multiple types and places of reuse.

In 1996, in order to facilitate water recycling and reuse in the Region, the Water Board adopted the General Water Reuse Requirements for Municipal Wastewater and Water Agencies, Water Board Order No. 96-011 (General Water Reuse Permit). This permit is applicable to producers, distributors, and users of non-potable recycled municipal wastewater throughout the Region. The intent of the General Water Reuse Permit is to streamline the permitting process and delegate, to the fullest extent possible, the responsibility of administrating water reuse programs to local agencies. Regulation under the General Water Reuse Permit requires submittal of a Notice of Intent (NOI) to the Water Board and written authorization from the Water Board’s Executive Officer.

Under the General Water Reuse Permit, water recycling and reuse have expanded rapidly throughout the Region. It is estimated that twenty wastewater or water distribution agencies in the Region will be operating under the General Water Reuse Permit by 2007.

In 2001, the State Legislature established the California Recycled Water Task Force (Task Force). The mission of the Task Force was to evaluate the current framework of state and local rules, regulations, ordinances, and permits to identify opportunities for and obstacles to the safe use of recycled water in California. The Task Force consisted of representatives from federal, state, and local agencies, private entities, environmental organizations, universities, and public-interest groups. The Task Force identified and adopted recommendations to address obstacles, impediments, and opportunities for California to increase its recycled water usage as described in the report “Water Recycling 2030, Recommendations of California’s Recycled Water Task Force."


Implementation of water recycling projects requires the involvement, approval, and support of a number of agencies, including state and local health departments, the Water Board, local POTWs and water districts, and land use planning agencies. Interagency coordination must be a priority of all parties involved in water recycling. Failure to coordinate activities can result in the inability to carry out water recycling projects in a timely, consistent, and cost-effective manner. The Water Board seeks cooperation and participation of professionals from the water recycling industry and the water, health, and regulatory agencies to assure the development of criteria that are both attainable and appropriate. To facilitate inter-/intra-regional recycling projects, interagency coordination is necessary when the wastewater agency produces recycled water outside of an interested water purveyor's service area. Effective communication and cooperation between agencies regarding distribution and service is vital and should begin early in the planning process. This will assure the water purveyor that there will be no duplication of service, enable interagency agreement on project development and implementation, and help avoid any unnecessary delays that could jeopardize a project.

Several regional water-recycling programs have been initiated in the Region to facilitate water reuse in contiguous areas. This has heralded a new way to implement water-recycling projects by focusing agencies toward regional collaboration, irrespective of jurisdictional boundaries. This has the effect of integrating water and wastewater planning to concurrently solve water supply and wastewater discharge problems, and will lead to more efficient water recycling projects by taking advantage of economics of scale. One such program is the South Bay Recycling Program in Santa Clara County. In addition, the North Bay Watershed Association was created, “to help regulated local and regional public agencies work cooperatively on water resource issues that impact areas beyond traditional boundaries in order to promote stewardship of the North Bay Watershed (Marin, Sonoma and Napa Counties).” The coordination and integration of water reuse activities in the North Bay is an important component of the Association’s functions.


One particular type of solid waste is wastewater sludge, a by-product of wastewater treatment. Raw sludge usually contains 93 to 99.5 percent water, with the balance being solids that were present in the wastewater and that were added to or cultured by wastewater treatment processes. Most POTWs treat the sludge prior to ultimate use or disposal. Normally this treatment consists of dewatering and/or digestion. In some cases, such as at the Palo Alto treatment plant, the sludge is incinerated.

Treated and untreated sludges often contain high concentrations of toxic metals and often contain significant amounts of toxic organic pollutants and pathogens. The storage and disposal of municipal sludges on land can result in degradation of ground and surface water if not properly performed. Therefore, sludge handling and disposal must be regulated.

On February 19, 1993, the U.S. EPA promulgated national standards regulating the use or disposal of non-hazardous sewage sludge (40 CFR Part 503, et.seq.). Part 503 regulations primarily affect sewage sludge (also known as "biosolids") use and disposal by incineration, surface disposal, and land application (including distribution and marketing). Part 503 regulations also establish pollutant limits, operational and maintenance practices, monitoring frequency, recordkeeping, and reporting requirements. The federal definition of sewage sludge includes domestic septage (from septic tanks, cesspool, portable toilet, etc.). Disposal in a municipal solid waste landfill (MSWLF) is not considered surface disposal. Thus, the MSWLF is not regulated by the national sewage sludge program.

The State of California has neither requested nor been granted the delegation of the federal sewage sludge management program at this time. Therefore, U.S. EPA will be responsible for implementation and enforcement of the national rule. Under the rule, facilities that must apply for a permit include the generators, treaters and disposers of sewage sludge. Nevertheless, 40 CFR Part 503 has, for the most part, been written to be self-implementing. This means that anyone who uses or disposes of sewage sludge regulated by 40 CFR Part 503 must comply with all the provisions of the rule, whether or not a permit has been issued.

State regulations of the handling and disposal of sludge are contained in Chapter 15 and DTSC standards for hazardous waste management. Prior to promulgation of the national rule, sewage sludge facilities were regulated by the Water Board through the issuance of site-specific waste discharge requirements. The Water Board may continue to regulate certain sewage sludge facilities when believed to be necessary for the protection of water quality.


As the population of the Region increases, demand for new development increases. In many cases, new development is within areas served by municipal sewer systems. However development is also occurring in outlying areas not served by existing sewerage agencies. In those instances, new discrete sewerage systems are being proposed. These are primarily onsite wastewater treatment and dispersal systems (onsite systems or septic systems) serving individual homes, but include community systems serving multiple residences. Today there are more than 110,000 onsite systems throughout the Region, and approximately 1,000 new systems are approved each year.

In response to these development pressures, the Water Board adopted a Policy on Discrete Sewerage Facilities in 1978 (Board Resolution No. 78-14). The Policy set forth guiding regulatory principles and the actions that the Water Board would take with respect to proposals for individual or community sewerage systems serving new development. The 1978 Policy was rescinded in 2014 when the State Water Board’s statewide Water Quality Control Policy for Siting, Design, Operation, and Maintenance of Onsite Wastewater Treatment Systems (OWTS Policy) was incorporated by reference into the Basin Plan (section 4.18.2) but relevant guiding principles and requirements from the 1978 Policy have been retained in section 4.18.1 to complement the OWTS Policy.


The Water Board will apply the following guiding principles to all wastewater discharges from discrete sewerage systems:

  • The system must be designed and constructed so as to be capable of preventing pollution or contamination of the waters of the state or creating nuisance;
  • The system must be operated, maintained, and monitored so as to continually prevent pollution or contamination of the waters of the state and the creation of a nuisance.

The Water Board requires an assessment of the cumulative impact of discharges from individual wastewater treatment and disposal systems on water quality and public health where the density of systems or geologic conditions are such that adverse impacts may occur. This assessment shall be included in the application submitted to local agencies for systems covered by the OWTS Policy conditional waiver or, if not covered by the conditional waiver, in the Report of Waste Discharge submitted to the Water Board.

The Water Board also requires that a public entity must assume legal authority and responsibility for the planning, design, financing, construction, operation, and maintenance of any new community wastewater treatment and dispersal system. Community systems are defined as collection sewers plus treatment facilities serving multiple discharges under separate ownership, such as small, pre-engineered and prefabricated packaged wastewater treatment plants or common septic tanks plus dispersal facilities. The responsible public entity must prepare acceptable operation, maintenance, revenue, and contingency plans for the wastewater treatment and dispersal facility. These plans shall be included in the application submitted to local agencies for systems covered by the OWTS Policy conditional waiver or, if not covered by the conditional waiver, in the Report of Waste Discharge submitted to the Water Board. In the absence of acceptable plans, the discharge will be prohibited.


The Water Board prohibits the discharge of wastes which threaten to cause water pollution, water quality degradation, or the creation of health hazards or nuisance condition. Requirements for siting, design, operation, maintenance, and management of onsite wastewater treatment systems are specified in the State Water Board’s OWTS Policy. The OWTS Policy, including future revisions, is incorporated into this Basin Plan and shall be implemented according to the policy’s provisions.

The OWTS Policy sets forth a tiered implementation program with requirements based upon levels (tiers) of potential threat to water quality. The OWTS Policy applies to: individual treatment and dispersal systems; community collection, treatment, and dispersal systems; and alternative collection, treatment, and dispersal systems that use subsurface dispersal. The OWTS Policy only applies to such systems with a projected flow of 10,000 gallons per day or less of domestic wastewater and, in some cases, high strength wastewater (not exceeding 900 mg/L BOD) from commercial food service buildings equipped with a properly sized and functioning oil/grease interceptor.

The OWTS Policy includes a conditional waiver of waste discharge requirements for onsite systems that are in conformance with the policy. Onsite wastewater treatment systems that do not meet the applicability criteria of the OWTS Policy or whose wastewater does not meet the quantity and quality specifications of the policy cannot receive coverage under the conditional waiver so these systems will be regulated by the Water Board through other regulatory means.


Graywater systems are a type of onsite systems that are used to manage only isolated domestic wastewaters that have not come in contact with toilet wastes. In 2009, the California Building Standards Commission approved revised California Graywater Standards (Graywater Standards). These standards developed by the California Department of Housing and Community Development, are codified at Title 24, CCR, Part 5, Chapter 16, and apply to all graywater systems statewide.

Pursuant to Health and Safety Code section 17922.12, “graywater” means untreated wastewater that has not been contaminated by any toilet discharge, has not been affected by infectious, contaminated, or unhealthy bodily wastes, and does not present a threat from contamination by unhealthful processing, manufacturing, or operating wastes. “Graywater” includes, but is not limited to, wastewater from bathtubs, showers, bathroom washbasins, clothes washing machines, and laundry tubs, but does not include wastewater from kitchen sinks or dishwashers.

The Graywater Standards specify the means by which graywater may be collected, filtered, and used either in irrigation systems or, if treated, certain indoor uses. The standards apply to both residential and commercial buildings. The Graywater Standards promote water conservation by facilitating re-use of laundry, shower, lavatory and similar sources of discharge for irrigation and/or indoor use. These revised standards allow certain types of systems to be installed without a building permit.

Cities and counties have authority to develop policies and procedures for the implementation of graywater programs. In developing these, consultation with the Water Board and local water districts can ensure that potential impacts on local water quality are taken into consideration.


Current estimates of annual sediment inflow to San Francisco Bay are 5.9 million cubic yards with 3.9 million cubic yards contributed through the Delta and 2.0 million cubic yards from Bay Area tributary streams. By the year 2000, ABAG has estimated that approximately 322,500 acres of land area will be converted to urban use. This is a 73 percent increase above the 1975 urbanized land area. This increase in urbanized land use can be expected to be the future source of much of the sediment that will reach the rivers, streams and channels and ultimately the Bay system each year.

Soil erosion and related water quality impacts may result from a wide variety of causes including construction, hillside cultivation, non-maintained roads, timber harvesting, improper hiking/ biking trail use, and off-road vehicles.

Natural erosion processes are accelerated when existing protective cover is removed before, during, and following construction and agricultural activities. Studies relate that erosion on land where construction activities are taking place is about 10 times greater than on land in cultivated row crops, 200 times greater than on pasture land, and 2,000 time greater than on timber land that has not been logged.

The exposure of the soil mantle to falling rain, overland and channelized flow, and the impact of equipment moving over the site results in the increased movement and loss of soil.

Damage from erosion and sedimentation can be categorized in the following ways:

  • Damage to construction sites;
  • Damage to stream channels;
  • Damage to water quality/beneficial uses;
  • Damage to public and private property; and
  • Damage to agricultural lands.

In most cases, the adverse results of human activities can be reduced and in some instances eliminated through the use of both structural and non-structural measures of various types that are properly employed at the appropriate time. The high cost of lost resources, resource replenishment and after-the-fact repair and maintenance make both pre-project erosion control planning and preventive maintenance necessary. The goals of and the program for erosion and sediment control are summarized below.


The goal of the Water Board’s Erosion and Sediment Control Program is to reduce and prevent accelerated (human-caused) erosion to the level necessary to restore and protect beneficial uses of receiving waters now significantly impaired, or threatened with impairment, by sediment.

This goal is to be attained through implementation of proper soil management practices. Voluntary implementation is encouraged, but enforcement authority will be exercised where beneficial uses of water are clearly threatened by poor soil management practices.


In May of 1980, the Water Board adopted two separate items to alert local governments to the Water Board's concern on erosion control problems related to construction activities. The first item was a statement of intent (Resolution No. 80-5) regarding erosion control which stated that the Water Board:

  • Recognizes that water quality problems are associated with construction related activities;
  • Recognizes ABAG's progress in developing erosion and sediment control regulatory programs and assistance to local governments to implement these programs;
  • Recognizes local governments power to adopt and implement these programs;
  • Intends to strengthen its position with regard to regulation of sediment and erosion control problems especially with regard to construction activities; and
  • Intends to take appropriate enforcement action pursuant to the California Water Code in cases where land development or other construction activity causes or threatens to cause adverse water quality impacts associated with erosion problems and intends to consider, during enforcement actions, whether local government negligently contributed to the problem due to failure to adopt and/or effectively enforce erosion control programs.

The second item was a memorandum of understanding negotiated with the Council of Bay Area Resource Conservation Districts that is intended to provide the following:

  • Assessment, control and monitoring of potential and existing soil erosion related water quality problems;
  • Improvement of coordination between the Resource Conservation Districts and the Water Board; and
  • Monitoring of local government progress on the adoption and implementation of erosion and sediment control ordinances.

The Water Board has recognized and encouraged the efforts that ABAG has made since mid-1980 in working with local Bay Area governments to improve their ordinance and regulatory programs on erosion and sediment control. ABAG's 1995 Manual of Standards for Erosion and Sediment Control Measures, which provides specific guidance to local governments, is an important tool for improving erosion and sediment control.

The Water Board intends to follow the guidelines listed below in regulating erosion and sedimentation for the protection of beneficial uses of water.

  1. Local units of government with land use planning authority should have the lead role in controlling land use activities that cause erosion and may, as necessary, impose further conditions, restrictions, or limitations on waste disposal or other activities that might degrade the quality of waters of the state.
  2. Best Management Practices (BMPs) should be implemented to reduce erosion and sedimentation and minimize adverse effects on water quality. A BMP is a practice or combination of practices determined to be the most effective and practicable means to prevent or reduce erosion and sediment related water quality degradation. Examples of control measures are contained in the Manual of Standards for Erosion and Sediment Control Measures. Further technical guidance can be obtained from the Resource Conservation Districts.
  3. Local governments should develop an effective erosion and sediment control ordinance and regulatory program. An effective ordinance and regulatory program must:
    • Be at least comparable to the model ordinances in ABAG's Manual of Standards for Erosion and Sediment Control Measures;
    • State that water quality protection is an explicit goal of the ordinance;
    • Require preparation of erosion and sediment control plans consistent with the Manual of Standards with specific attention to both off-site and on-site impacts;
    • Provide for installation of approved control measures no later than October 15 of each year; and
    • Have provisions for site inspections with follow up at appropriate times, posting of financial assurances for implementation of control measures, and an enforcement program to assure compliance with the ordinance.
  4. All persons proposing alterations to land (over five acres) are required to file a Report of Waste Discharge and/or and Erosion Control Plan with the Water Board. A statewide general NPDES permit aimed at minimizing erosion from the proposed activities has been issued.

    In addition, the Water Board may find that any water quality problems caused by erosion and sedimentation for such a project were due to the negligent lack of an adequate erosion control ordinance and enforcement program by the local permitting agency. Such a finding of negligence could subject a permitting agency to liability for indemnification to a developer if civil monetary remedies are recovered by the state.

  5. The Water Board may take enforcement action pursuant to the California Water Code to require the responsible persons (including local permitting agencies) to clean up and abate water quality problems caused by erosion and sedimentation in the event that the local permitting agency fails to take the necessary corrective action.



Dredging and dredged sediment disposal in the San Francisco Bay Area is an ongoing activity because of continual shoaling which impedes navigation and other water dependent activities. Large volumes of sediment are transported in the waters of the Sacramento and San Joaquin Rivers which drain the Central Valley. The average annual sediment load to the San Francisco Bay system from these two rivers is estimated to be eight million cubic yards. Of this amount, some four million cubic yards is transported out of the Bay through the Golden Gate. The remaining four million cubic yards is circulated and/or deposited in the Bay. In addition, some two and one-half million cubic yards are deposited into the Bay from local watersheds. The largest volume of sediment that affects the Bay is the approximately 100 million cubic yards that are re-suspended in the water column by the actions of tide, wind and currents.

Dredging is generally necessary to maintain the beneficial use of navigation. The trend towards increasingly larger vessels also necessitates increased channel depths in the shipping channels.

Disposal of the majority of dredged material from San Francisco Bay has historically been at designated disposal sites in San Francisco Bay. This practice dates back to at least the beginning of the 20th century. Currently there are three such multi-user disposal sites designated by the U.S. Army Corps of Engineers (USACE, or Corps): the Alcatraz (SF-11), San Pablo Bay (SF-10), and Carquinez (SF-9) Disposal Sites. A fourth site (Suisun Bay, SF-16) is maintained for Corps use exclusively for material from dredging of the Suisun Bay and New York Slough federal channels.

Annual maintenance dredging of shipping channels, harbors, and marinas in the San Francisco Bay results in disposal of between two and eight million cubic yards of dredged material at in-bay disposal sites. All designated aquatic dredged material disposal sites are operated as “dispersive” sites, that is, material disposed at the sites is intended to disperse and be carried by currents out to sea. Additionally, one of the management practices is to only allow material to be disposed of at disposal sites downstream of the dredging sites, with the objective of moving sediments away from dredging sites and out of the Bay. While the overall hydrodynamics of the Bay are not completely understood it is clear that the fate of material placed at in-bay disposal sites is dependent upon material type, disposal volume, and disposal frequency.

Since 1994, when the U.S. EPA designated the Deep Ocean Disposal Site approximately 50 miles offshore of San Francisco, approximately 6 million cubic yards of dredged material have been disposed of there.

Dredged material has also been used as fill for wetland restoration projects, for levee maintenance, and as daily cover for landfills. Volumes for these, and other beneficial reuse projects, have totaled approximately 2 million cubic yards over the past 9 years.


The Corps of Engineers issues federal permits for dredging projects pursuant to Section 404 of the Clean Water Act. The U. S. EPA provides oversight of the Corps’ regulatory program.

As a part of the Section 404 permitting process, the dredging permit applicant must seek water quality certification from the State of California, in accordance with Section 401 of the Clean Water Act. The Water Board reviews the proposed project, then may grant or deny certification. Additionally, the Water Board may choose to act under the authority of the state Porter Cologne Water Quality Control Act, by issuing waste discharge requirements for the project in conjunction with the water quality certification.

Water quality certifications and waste discharge requirements often contain conditions to protect water resources that the permittee must meet during the term of the permit.

The San Francisco Bay Conservation and Development Commission (BCDC) also regulates dredging and disposal under the provisions of the McAteer-Petris Act.

Projects involving the use of sovereign lands of the state may be subject to the lease or permitting requirements of the State Lands Commission.


In the early 1980s, the problems associated with heavy reliance on in-Bay disposal sites became apparent, including navigational problems associated with the “mound” of dredged material at the Alcatraz disposal site, as well as potential environmental problems associated with disposal and dredging activities in general. These conditions led to the creation of the Long Term management Strategy for the Placement of Dredged Material in the San Francisco Bay Region (LTMS).

The LTMS program began in 1990, when the Water Board joined with USACE, U. S. EPA, BCDC, the State Board, and representatives from the dredging and environmental communities to ensure adequate dredged material disposal and reuse capacity and protection of aquatic resources over a 50-year planning period. The adopted goals for the program (Table 4-11) reflect this purpose. The primary focus of the LTMS is on the various dredged material disposal options and their related impacts. The LTMS was also initiated to maximize beneficial reuse of dredged material, improve coordination of the agencies governing these activities, and ensure a more predictable regulatory framework.

The LTMS examined several possible long-term dredged material management strategies. The LTMS Policy Environmental Impact Statement/Programmatic Environmental Impact Report (LTMS EIS/EIR, Volume I, Volume II-Appendices, Volume III Comments and Responses) selected as the preferred alternative a reduction in the reliance on in-Bay disposal. The ultimate goal of this alternative is a “low” volume of disposal at in-Bay sites (20% of historical average dredging volumes), and an increased reliance on ocean disposal and beneficial reuse of dredged material (with the remaining material split evenly between these two options). The LTMS EIS/EIR was certified by the USACE and U.S. EPA in July 1999 and by the State Board in November 1999, thus beginning the implementation of the preferred alternative.

During the preparation of the LTMS EIS/EIR, the LTMS agencies consulted with the United States Fish and Wildlife Service (USFWS), the National Marine Fisheries Service (NMFS), and the California Department of Fish and Game (CDFG) regarding potential impacts of dredging and dredged material disposal to sensitive biological resources. These resource agencies, in conjunction with the LTMS agencies, developed a list of restrictions for such projects to protect critical habitat for special status and important commercial and recreational species.

The LTMS EIS/EIR identified the overall future disposal management strategy (i.e. reduced in-Bay disposal volumes at the designated dispersive sites). The LTMS Management Plan contains specific guidance that will be used to implement the preferred alternative by each of the LTMS agencies. The Management Plan will be reviewed and updated every three years to reflect changing statutory, regulatory, technical, or environmental conditions. The Basin Plan dredging policies will be updated, as necessary, in conjunction with Management Plan updates.


Most dredging and dredge material disposal operations cause localized and ephemeral impacts with related biological consequences (Table 4-12). In the 1980s it was determined that the Alcatraz disposal site was accumulating significant amounts of material, with the depth of the site going from the original 110 feet to 30 feet. The mounding at the disposal site ultimately became a threat to navigation. The Corps eventually dredged the Alcatraz site to increase the depth, redistributing the material within the disposal area several times between 1984 and 1986.

In September of 1988, Water Board staff circulated and presented an issue paper entitled "A Review of Issues and Policies Related to Dredge Spoil Disposal in San Francisco Bay." The issue paper discussed the major environmental concerns posed by dredged sediment disposal in San Francisco Bay, namely: (1) mounding at the Alcatraz disposal site which posed a navigational hazard and has the potential to alter circulation patterns in the Bay; (2) the disposal of increasingly large amounts of material has the potential to alter benthic and shoreline habitats and to increase water column turbidity; and (3) the resuspension of dredged sediments may increase contaminant bioavailability. The issue paper presented a range of alternative strategies for the Water Board to consider. Public and agency testimony was received by the Water Board during hearings on September 15, 1988 and October 19, 1988. Agencies testifying included the Corps, U.S. Environmental Protection Agency (USEPA), and California Department of Fish and Game (CDFG). In the issue paper, Water Board staff recommended that the Water Board consider adopting quantity and quality limits for the disposal of dredged sediment at unconfined aquatic disposal sites within San Francisco Bay.

Additionally, the Water Board and the Corps took steps to prevent further "mounding" at the region's single largest disposal site, the Alcatraz site. In 1989, the Water Board adopted volume targets which served to prevent over-filling of the region's three aquatic disposal sites. BCDC also revised its policies to restrict in-bay disposal. These volumes were reduced further for the Alcatraz disposal site (SF-11) in 1993 when the USACE issued Public Notice 93-3.


While the Water Board remains concerned about the impacts of both polluted and clean sediments on the San Francisco Estuary, much of the sediment disposed of in the Region is not polluted and could be used in beneficial ways (termed "reuse"). One of these uses involves the restoration of tidal marshes in areas which were once part of the Bay. These areas, known as diked historic baylands, were once open to the tides and were thriving salt marsh and mudflat ecosystems (further discussion under "Wetlands Protection and Management" section). Decades of land "reclamation," first initiated in the 1800s resulted in diked agricultural lands, the land surface of which has subsided for a variety of reasons.

In order to foster growth of marsh vegetation, and proper slough channel formation, the new marsh must be built near mean high tide. In many cases it will be beneficial to place a layer of sediment across the site so as to raise the elevation of the land surface to a point near the mean tide line. LTMS studies have examined the environmental, engineering and economic considerations that are involved in restoring certain sites. The studies commissioned by LTMS have shown that, given current laws and policies, placement of dredged sediment at wetland restoration projects may cost more than traditional in-Bay disposal, but less than ocean disposal.


Winter Island, located in the western Delta, near Pittsburg, is operated as a duck club by the local Reclamation District. In 1998, the Reclamation District, in need of material to repair levees, partnered with the Corps of Engineers, and accepted over 200,000 cubic yards of sandy dredged material from the Corps' dredging of the federal Suisun Bay Channel. In 1999, an additional 225,000 cubic yards from the Suisun Bay Channel project was placed on the site, along with approximately 30,000 cubic yards of finer-grained material from the Port of San Francisco. The Reclamation District estimates that they will have a long-term need for fine-grained dredged material, of about 100,000 cubic yards per year.

Other Delta islands are also in need of material for levee repair. For example, the Corps is currently exploring the possibility of taking material from the Suisun Bay Channel to Sherman Island. Cooperation with the Department of Water Resources, the Central Valley Regional Water Quality Control Board, and the CalFed program may provide additional opportunities for reuse of dredge material in the future.


The overall policy for dredging and disposal of dredged sediment includes a reduction of in-bay disposal volumes and an increased emphasis on beneficial reuse of dredged material. The most likely beneficial reuse of dredged material is wetland restoration projects or for levee maintenance and repair. Additional capacity for dredged material is available at the deep ocean disposal site designated by U.S. EPA in 1994. The goal of the policies below is to reduce in-bay disposal volumes to approximately 20% of recent historical dredging volumes, to about 1 million cubic yards per year.

Dredging and dredged material disposal should be conducted in an environmentally and economically sound manner. Dredgers should reduce disposal in the Bay over time to achieve the LTMS goal of one million cubic yards, or less, per year. The LTMS agencies will implement a system of disposal allocations for the designated disposal sites to individual dredgers to achieve the LTMS goal only if voluntary efforts are not effective in reaching this goal. NEED FOR REGIONAL AND LOCAL MONITORING

The Regional Monitoring Program (RMP) provides information on the regional-scale effects of contaminants in the Bay. The Water Board is evaluating whether additional, more localized monitoring to isolate the effects of the disposal of dredged material in the Bay is needed. In the interim, existing sediment evaluation procedures (See Policy, below) and monitoring and management efforts at the in-Bay disposal sites are protective of the beneficial uses of the Bay. MATERIAL DISPOSAL RESTRICTION

Materials disposed of at approved aquatic dredged material disposal sites shall be restricted to dredged sediment. Disposal of rock, timber, general refuse and other materials shall be prohibited. Additional specific requirements regarding material type and dredging and disposal mechanisms may be implemented as required, based on ongoing site monitoring and adaptive management. VOLUME TARGETS INDIVIDUAL DISPOSAL SITES

Volume targets for each disposal site were developed based on understandings of sediment dynamics and historical information regarding disposal volumes (Table 4-14).

In addition, the Water Board establishes a volume target of 0.2 million cubic yards per year for the Suisun Bay Channel disposal site and restricts its use to Corps maintenance dredging. The San Francisco Bar site is used for disposal of material from the bar channel. The use of the San Francisco Bar disposal site is regulated under the Marine Protection, Research, and Sanctuaries Act (MPRSA). OVERALL IN-BAY DISPOSAL

Although the overall in-Bay disposal goal is one million cubic yards per year, the LTMS recognized that the inherent variability in dredging operations and needs and other factors may impact dredgers’ ability to achieve this goal. The LTMS therefore established a slightly higher long-term in-Bay disposal volume target of 1.25 million cubic yards per year. Total in-Bay disposal volumes should decrease according to the schedule identified in Table 4-15, until the long-term LTMS target of 1.25 million cubic yards per year is attained.

In addition to the total volume specified in Table 4-15:

  1. Material from small dredging projects (see below) will, in general, be exempt from restrictions on in-Bay disposal if it is demonstrated through an alternatives analysis that there are no practical alternatives to in-Bay disposal, and

  2. A contingency volume of 250,000 cubic yards per year will be established for “emergencies” or for years when sedimentation or other factors result in unanticipated material volumes. A dredging emergency is a situation that poses an immediate danger to life, health, property, or essential public service and that demands action by the Board more quickly than the Board’s normal permit procedures would allow. VOLUME TARGET IMPLEMENTATION INDIVIDUAL DISPOSAL SITES

The Water Board will consider denial of water quality certification for:

  1. Any project proposing to place material at a disposal site for which the annual or monthly volume target, as defined in Table 4-14, has been exceeded; and
  2. Any project that does not provide an adequate alternatives analysis showing that there are no practicable alternatives to in-Bay disposal.

Small project proponents may apply for an exemption to monthly or annual volume targets. A small project is defined as a facility or project whose design depth does not exceed 12 feet Mean Lower Low Water (MLLW) with an annual average disposal volume of less than 50,000 cubic yards. The project proponent must demonstrate that:

  1. The additional burden of using an alternative to in-Bay disposal placed upon the applicant would be inordinate relative to the beneficial uses protected; and
  2. The alternatives analysis indicates that there are no practical alternatives to in-Bay disposal. OVERALL IN-BAY DISPOSAL

A voluntary program will be instituted to attain the overall in-Bay disposal targets adopted by the LTMS EIS/EIR with the majority of maintenance material from Corps of Engineers projects being used in wetland restoration projects or taken to the ocean disposal site. As part of the voluntary program, other dredgers will make efforts to use alternatives to in-Bay disposal.

Progress towards the goal will be evaluated both on an annual basis and every three years, based on the three-year average volume of in-Bay disposal. Should this voluntary program fail to provide progress toward the goal in the reviews outlined above, a mandatory allocation program will be considered. The institution of the mandatory allocation process will occur as outlined below and the determination to rescind mandatory allocation, if imposed, will be a symmetric process.

The Water Board will consider the imposition of mandatory allocation in a Water Board hearing. In making its decision regarding disposal allocations, the Water Board will confer with the LTMS agencies and consider the factors affecting the need for allocations in light of progress towards the long-term goal adopted by the LTMS EIS/EIR, including (1) the status of alternatives to in-Bay disposal and cooperative efforts to implement them, (2) exigencies that hamper the use of alternative sites, and (3) other relevant factors. If the Water Board votes to impose mandatory allocations, the mandatory allocation program will be regulated through the issuance of general Waste Discharge Requirements for small- and medium-category dredging projects and through separate Waste Discharge Requirements for all USACE dredging projects. If in place, rescission of the mandatory allocation program would be considered if the three-year average disposal volume was lower than the target volumes as identified in Table 4-15, unless, after review by the Water Board in a public hearing, the Water Board votes to not rescind mandatory allocations. Both the institution and rescission of the mandatory allocation program would be discretionary actions of the Water Board, and thus subject to review pursuant to CEQA under the Water Board’s functionally-equivalent process. USE OF TESTING GUIDELINES

In February of 1998, the Corps and U.S. EPA published Evaluation of Dredged Material Proposed for Discharge in Waters of the U.S. – Testing Manual, Inland Testing Manual (ITM). The ITM has been adopted by the LTMS agencies as the framework for the evaluation of the suitability of dredged material for in-Bay disposal. It provides comprehensive guidance to dredging permit applicants on sampling and testing of sediment proposed for disposal in waters of the United States, pursuant to Section 404 of the Clean Water Act. Disposal at the in-Bay disposal sites is subject to this guidance. The ITM outlines a tiered approach to sediment testing, similar to the existing Ocean Disposal Testing Manual, or “Green Book,” the federal guidance document for testing for ocean disposal (pursuant to MPRSA). The Water Board’s Executive Officer will require evaluation of sediments proposed for in-Bay disposal according to the ITM, before issuing authorizations for such disposal.

The ITM was intended to only address testing of material for aquatic disposal and does not provide a protocol for upland disposal. Water Board staff have developed a document, “Beneficial Reuse of Dredged Materials: Sediment Screening and Testing Guidelines,” to assist project planners with developing testing procedures for beneficial reuse projects, including wetland restoration, levee maintenance, and construction fill. The document also provides general sediment screening guidelines for these uses. However, disposal of dredged material for beneficial reuse will be subject to site-specific testing requirements and material suitability criteria that will be defined in Water Board Orders.

The Water Board is working in cooperation with other LTMS agencies to develop a regional implementation manual which will detail testing requirements for all three disposal environments.

The Executive Officer, following consultation with other agencies, will periodically review and update all testing procedures. The Executive Officer may require additional data collection beyond the tiered-testing procedures on a case-by-case basis. ENVIRONMENTAL WINDOWS

The Water Board will restrict dredging or dredge disposal activities during certain periods ("windows") in order to protect the beneficial uses of San Francisco Bay. These beneficial uses include water contact recreation; ocean, commercial, and sport fishing; marine habitat; fish migration; fish spawning; shellfish harvesting; and estuarine habitat.

These restrictions may include, but are not limited to those specified by USFWS and NMFS in their review of the LTMS programmatic EIS/EIR pursuant to Section 7 of the Endangered Species Act, and will incorporate any requirements from project specific consultations. IMPACTS AT DREDGE SITE

The Water Board may require additional documentation and inspections during dredging activities in order to ensure that dredgers minimize impacts at the dredging location. Water Quality Certifications or waste discharge requirements may contain additional conditions to address barge overflow and other impacts at the dredging site. Permit conditions may include:

  1. Special reporting procedures for the hydraulic pumping of dredged material into transport scows prior to disposal (marina slip applications);
  2. Evidence of compliance with the conditions described in, above;
  3. Time limit on the overflow from hopper-type hydraulic dredges in order to obtain an economical load; or
  4. Precautions to minimize overflow and spillage from the dredging vessel when in-route to the authorized disposal site. (Appreciable loss during transit shall be considered unauthorized disposal, or "short dumping" and such occurrences are subject to enforcement by the Water Board or other applicable state or federal agencies.) POLICY ON LAND AND OCEAN DISPOSAL

The Water Board shall continue to encourage land and ocean disposal alternatives whenever practical. Water Board staff have determined that there should be a high priority placed on disposing of dredged sandy material upland. At a minimum, incentives should be developed to limit disposal of any such material with a market value to upland uses. Staff may condition certifications so as to encourage upland reuse of high value sediments. Staff will also continue to work with staff from the Central Valley Regional Water Quality Control Board to provide appropriate options for material use in levee maintenance in the delta or for use on delta islands, as appropriate. POLICY ON DREDGED MATERIAL DISPOSAL PERMIT COORDINATION

The Water Board will implement these measures through its issuance of Waste Discharge Requirements, Water Quality Certification under Section 401 of the Clean Water Act or other orders. In addition, the Water Board may require pre- and post-dredge surveys to determine disposal volumes and compliance with permit conditions. In order to better manage data and reduce paper files, Water Board staff may request, but not require, that applicants submit testing and other project data in a specific electronic format.

Water Board staff have been participating in a coordinated permitting process, the Dredged Material Management Office (DMMO), since 1995. The DMMO consists of staff representatives of the Water Board, BCDC, U. S. EPA, USACE, and the California State Lands Commission, with active participation by the California Department of Fish and Game and the National Marine Fisheries Service as commenting resource agencies. The DMMO meets regularly to review permit applications and sediment testing plans and results and to make recommendations on proposed dredging projects. While each agency retains its separate authority the agency representatives strive to provide clear and coordinated guidance to applicants and to reach consensus-based recommendations.


The Water Board oversees water quality problems associated with over 150 inactive and active mining and mineral producers in the Region, as described below.


Over 50 abandoned or inactive mines have been identified within the Region (Table 4-16 and Figure 4-5). The mineral resources extracted include mercury, magnesite, megnesium salts, manganese, pyrite, coal, copper, silver, and gold. A large percentage of the mining activities took place from 1890-1930, although some areas were mined as recently as 1971. The size of these mines varies from relatively small surface mines of less than half an acre to the world's second largest mercury mine, the New Almaden District, located in Santa Clara County.

Water quality problems associated with mining activities can be divided into three categories:

  • Erosion and sediment discharges from surface mines and ore tailings piles;
  • Acid or otherwise toxic aqueous discharge from underground mines, ore tailings, slag, or other mining processes; and
  • Atmospheric deposition, such as releases from stacks carried downwind from mine sites.

Problems of erosion and sediment discharged from mined areas may be intensified due to the fact that sediment from ore-rich areas typically contain high concentrations of metals. Biological processes which take place in lake and stream bottom sediments may allow for these pollutants to be released in a form that more readily bioaccumulates in the food chain.

Water quality and aquatic toxicity monitoring data suggests that the beneficial uses of a number of water supply reservoirs, creeks, and streams in the Region have been impacted as a result of past mining activities. Threatened beneficial uses of lakes, streams, bays and marshes due to mining activities so far identified in the Region include: fish migration, fish spawning, shellfish harvesting, wildlife habitat, preservation of rare and endangered species, cold and warm freshwater habitat, and water contact recreation. In response to these findings, the Water Board conducted surveys to locate abandoned and operating mines in the Region. The results of the surveys are compiled in the 1998 report titled, "San Francisco Bay Regional Water Quality Control Board Mines Report."

In many cases, the adverse results of previous surface mining activities can be reduced, and in some cases eliminated, through appropriate erosion and sediment control practices. The U.S. Natural Resource Conservation Service (NRCS, formerly Soil Conservation Service) has developed a Resource Management System for Surface Mined Areas. This management system references practices and treatment alternatives needed to address the following:

  • Erosion control practices that route surface water run-off at non-erosive velocities and reduce soil movement by wind or water to within acceptable limits;
  • Maintenance of adequate water quality and quantity for planned uses and to meet federal, state, and local requirements;
  • Pollution control to meet federal, state, and local regulations; and
  • A system of planned access and/or conveyance that is within local regulations and meets the needs for the intended use.

In 1980, a memorandum of understanding (MOU) was negotiated with the Council of Bay Area Resource Conservation Districts in order to provide for assessment and monitoring of potential and existing soil erosion-related water quality problems, and identification of control measures. It was agreed that local units of government should have the lead role in controlling land use activities that cause erosion. Controls measures include the implementation of BMPs. The Resource Management System for Surface Mined Areas developed by NRCS specifically references BMPs determined to be the most effective and practicable means of preventing or reducing erosion and sediment-related water quality degradation resulting from surface mining activities.


There are approximately 100 active quarries and mineral producers within the Region. The primary commodities produced include clay, salt, sand and gravel, shale, and crushed stone. Water quality problems associated with active mineral production generally consist of erosion and sediment discharge into nearby surface water bodies and wildlife habitat destruction.

Mining activities are in part regulated under the Surface Mining and Reclamation Act of 1975. This Act requires all mine operators to submit a reclamation plan to the California Geological Survey (formerly California Department of Conservation, Division of Mines and Geology) and the recognized lead local agency for the area in which the mining is taking place. Recognized lead local agencies for the Region include county planning and public works departments. Additionally, some local planning departments regulate mining activities through the issuance of conditional land use permits. The goal of each reclamation plan is to assure that mined lands are reclaimed to a usable condition that is readily adaptable for alternate land uses and creates no danger to public health and safety. The current permitting process places very little emphasis on the need to protect beneficial uses of surface and groundwater.

Under Title 23, CCR, Chapter 15, Article 7, the Water Board has the authority to regulate mining activities that result in a waste discharge to land through the use of WDRs. Additionally, the federal NPDES stormwater regulations (40 CFR Parts 122, 123, and 124) require active and inactive mining operations to obtain NPDES permit coverage for the discharge of stormwater polluted by contact with any overburden, raw material, intermediate products, finished products, byproducts, or waste products.


The Water Board’s goal for its mining program is to restore and protect beneficial uses of receiving waters now impaired, or threatened with impairment, resulting from past or present mining activities. This goal will be attained by the coordinated effort of the Water Board, NRCS, the Council of Bay Area Resource Conservation Districts, the California Geological Survey, and lead local government agencies through the implementation of a mineral production and mining management program.


1. The Water Board intends to continue to work closely with Resource Conservation Districts and NRCS to identify all existing and abandoned mines and mineral production sites in the Region. Responsible parties will be identified. If needed, potential funding alternatives for cleanup activities will also be identified. Sites will be prioritized based on existing and potential impacts to water quality and size.

2. The Water Board will require an NPDES permit for the discharge of polluted stormwater from active and inactive mining operations, as defined in NPDES stormwater regulations. The Water Board will consider issuing individual permits or a general permit for such discharges, or will otherwise allow coverage under the State Water Board general permit for stormwater discharges associated with industrial activity as described in Section 4.14 Urban Runoff Management, Industrial Activity Control Program. Requirements of the notice of intent to be covered under the general permit(s) and the schedule for submittal will be established in the permit(s).

3. The responsible party or operator of each site discharging, or potentially discharging waste to land shall be required to submit a Report of Waste Discharge to the Water Board. Submittal of a Report of Discharge will be requested by the Water Board pursuant to the Water Code Section 13267. Requests will be made on a site-by-site basis and based on priority. A Report of Waste Discharge shall consist of a “Site Closure Plan” and an “Operation and Management Plan” for active sites, as described below:

  • Each plan shall be designed to ensure short- and long-term protection of beneficial uses of receiving waters.
  • The “Closure Plan” shall address site restoration and long-term maintenance and monitoring, which may include a financial guarantee to ensure that adequate funds are available for proper site closure.
  • The “Operation and Management Plan” shall address stormwater runoff and erosion control measures and practices.
  • Each plan will be evaluated in regard to potential impacts to beneficial uses of receiving waters. WDRs will be issued or conditionally waived at the discretion of the Water Board based on the threat to water quality and the effectiveness of identified and implemented control measures and the effectiveness of local agency oversight.


The discharge of wastes from pleasure, commercial, and military vessels has been a water quality concern of the Water Board since 1968 when Resolution No. 665 was adopted, which suggested that the federal government regulate waste discharges from vessels. In 1970 the Water Board adopted Resolutions 70-1 and 70-65 on vessel wastes. The first urged BCDC to condition marina permits for new or expanded marinas to include pumpout facilities, dockside sewers, and restroom facilities. Resolution 70-65 recommended that vessel wastes be controlled in such a manner through legislative action.

In 1982, the Water Board conducted a study that found high levels of coliform in the vicinity of several marinas in Marin County’s Richardson Bay. Subsequently, the Water Board adopted a prohibition against discharge of any kind into Richardson Bay. A regional agency was formed to implement and enforce this prohibition.

There is an ongoing effort to construct, renovate, and improve pumpout facilities at marinas and ports around the region. The goal of these efforts is to increase the accessibility of these facilities to boaters and reduce pollution from vessel wastes.


Wetlands and related habitats comprise some of the Region's most valuable natural resources. Wetlands provide critical habitats for hundreds of species of fish, birds, and other wildlife; offer open space; and provide many recreational opportunities. Wetlands also serve to enhance water quality, through such natural functions as flood control and erosion control, stream bank stabilization, and filtration and purification of surface water.

The Water Board will refer to the following for guidance when permitting or otherwise acting on wetland issues:

  • Governor’s Executive Order W-59-93 (signed August 23, 1993; also known as the California Wetlands Conservation Policy, or the "No Net Loss" policy);
  • Senate Concurrent Resolution No. 28; and
  • Water Code Section 13142.5 (applies to coastal marine wetlands).

The goals of the California Wetlands Conservation Policy include ensuring "no overall net loss,” achieve a “long-term net gain in the quantity, quality, and permanence of wetlands acreage and values ...", and reducing "procedural complexity in the administration of state and federal wetlands conservation programs."

Senate Concurrent Resolution No. 28 states, "It is the intent of the legislature to preserve, protect, restore, and enhance California's wetlands and the multiple resources which depend on them for the benefit of the people of the state."

Water Code Section 13142.5 states, "Highest priority shall be given to improving or eliminating discharges that adversely affect ... wetlands, estuaries, and other biologically sensitive sites."

The Water Board may also refer to the Estuary Project’s Comprehensive Conservation and Management Plan (June, 1994) for recommendations on how to effectively participate in a Region-wide, multiple-agency wetlands management program.


Consistent with the California Wetlands Conservation Policy, the Water Board participated in the preparation of two planning documents for wetland restoration around the Estuary: Baylands Ecosystem Habitat Goals (1999) and Baylands Ecosystem Species and Community Profiles (2000), together known as the Habitat Goals reports. The Habitat Goals reports provide a starting point for coordinating and integrating wetland planning and regulatory activities around the Estuary. The Habitat Goals reports identify and specify the beneficial uses and/or functions of existing wetlands and suggest wetland habitat goals for the baylands,defined in the Habitat Goals reports as shallow water habitats around the San Francisco Bay between maximum and minimum elevations of the tides. The baylands ecosystem includes the baylands, adjacent habitats, and their associated plants and animals. The boundaries of the ecosystem vary with the bayward and landward movements of fish and wildlife that depend upon the baylands for survival. The Habitat Goals reports were the non-regulatory component of a conceptual regional wetlands management plan from the mid-1990’s.


Beneficial uses of water are defined in Chapter 2 Beneficial Uses and are applicable throughout the Region. Chapter 2 also identifies and specifies the beneficial uses of 34 significant marshes within the Region (Table 2-3). Chapter 2 indicates that the listing is not comprehensive and that beneficial uses may be determined site-specifically. In making those site-specific determinations, the Water Board will consider the Habitat Goals reports, which provide a technical assessment of wetlands in the Region and their existing and potential beneficial uses. In addition to the wetland areas identified in Chapter 2, the Habitat Goals reports identified additional wetlands in the Region as having important habitat functions. Because of the large number of small and non-contiguous wetlands within the Region, it is not practical to specify beneficial uses for every wetland area. Therefore, beneficial uses will frequently be specified as needed for a particular site. This section provides guidance on how beneficial uses will be determined for wetlands within the Region.

Information contained in the Habitat Goals reports, the National Wetlands Inventory (NWI) prepared by the U.S. Fish and Wildlife Service (USFWS), and in the scientific literature regarding the location and areal extent of different wetland types will be used as initial references for any necessary beneficial use designation. The NWI is the updated version of the USFWS's Classification of Wetlands and Deepwater Habitats of the United States (Cowardin, et al. 1979), which is incorporated by reference into this plan, and was previously used by the Water Board to identify specific wetland systems and their locations. The updated NWI or other appropriate methods will continue to be used to locate and identify wetlands in the Region. A matrix of the potential beneficial uses that may be supported by each USFWS wetland system type is presented in Table 2-4.

It should be noted that, while the Habitat Goals reports and USFWS's NWI wetlands classification system are useful tools for helping to establish beneficial uses for a wetland site, it is not suggested that these tools be used to formally delineate wetlands.


Hydrology is a major factor affecting the beneficial uses of wetlands. To protect the beneficial uses and water quality of wetlands from impacts due to hydrologic modifications, the Water Board will carefully review proposed water diversions and transfers (including groundwater pumping proposals) and require or recommend control measures and/or mitigation as necessary and applicable.


The beneficial uses of wetlands are frequently affected by diking and filling. Pursuant to Section 404 of the Clean Water Act, discharge of fill material to waters of the United States must be performed in conformance with a permit obtained from the U.S. Army Corps of Engineers (Corps) prior to commencement of the fill activity. Under Section 401 of the Clean Water Act, the state must certify that any permit issued by the Corps pursuant to Section 404 will comply with water quality standards established by the state (e.g., Basin Plans or statewide plans), or can deny such certification, with or without prejudice. In California, the State and Regional Water Boards are charged with implementing Section 401. California’s Section 401 regulations are at Title 23, CCR, Division 3, Chap 28, Sections 3830-3869. Pursuant to these regulations, the Water Board and/or the Water Board’s Executive Officer have the authority to issue or deny Section 401 water quality certification. The certification may be issued with or without conditions to protect water quality.

The Water Board has independent authority under the Water Code to regulate discharges of waste to wetlands (waters of the state) that would adversely affect the beneficial uses of those wetlands through waste discharge requirements or other orders. The Water Board may choose to exercise its independent authority under the Water Code in situations where there is a conflict between the state and the Corps, such as over a jurisdictional determination or in instances where the Corps may not have jurisdiction. In situations where there is a conflict between the state and the Corps, such as over a jurisdictional determination or in instances where the Corps may not have jurisdiction, the Water Board may choose to exercise its independent authority under the Water Code.

The regulation of “isolated" waters determined not to be waters of the U.S. is one such instance where the Corps does not have jurisdiction. The U. S. Supreme Court, in its 2001 decision in Solid Waste Agency of Northern Cook County v. U. S. Army Corps of Engineers (the “SWANCC decision”) determined that certain isolated, non-navigable waters are not waters of the U.S., but are the province of the states to regulate. The Water Code provides the State and Regional Water Boards clear authority to regulate such isolated, non-navigable waters of the state, including wetlands. To address the impacts of the SWANCC decision on the waters of the state, the State Water Board issued Order No. 2004-0004-DWQ in 2004, General WDRs for dredged or fill discharges to waters deemed by the Corps to be outside of federal jurisdiction. It is the intent of these General WDRs to regulate a subset of the discharges that have been determined not to fall within federal jurisdiction, particularly those projects involving impacts to small acreage or linear feet and those involving a small volume of dredged material.

Order No. 2004-004-DWQ does not address all instances where the Water Board may need to exercise its independent authority under the Water Code. In such instances, dischargers and/or affected parties will be notified with 60 days of the Water Board's determination and be required to file a report of waste discharge.

For proposed fill activities deemed to require mitigation, the Water Board will require the applicant to locate the mitigation project within the same section of the Region, wherever feasible. The Water Board will evaluate both the project and the proposed mitigation together to ensure that there will be no net loss of wetland acreage and no net loss of wetland functions. The Water Board may consider such sources as the Habitat Goals reports, the Estuary Project's Comprehensive Conservation and Management Plan, or other approved watershed management plans when determining appropriate "out-of-kind" mitigation.

The Water Board uses the U.S. EPA's Section 404(b)(1), "Guidelines for Specification of Disposal Sites for Dredge or Fill Material," dated December 24, 1980, which is incorporated by reference into this plan, in determining the circumstances under which wetlands filling may be permitted.

In general, it is preferable to avoid wetland disturbance. When this is not possible, disturbance should be minimized. Mitigation for lost wetland acreage and functions through restoration or creation should only be considered after disturbance has been minimized.

Complete mitigation projects should be assessed using established wetland compliance and ecological assessment methods, such as the Wetland Ecological Assessment (WEA) and the California Rapid Assessment Method (CRAM).


Oil spills can cause severe and extensive damage to the environment. Fortunately, the petroleum industry has been improving its safety record in oil transfer operations - the step in petroleum handling where spills are most likely to occur. The volume of oil spilled during transfer operations has decreased since 1975.

This improvement is due to:

  • U.S. Coast Guard regulations for oil transfer operations;
  • State Lands Commission guidelines for petroleum facility operations manuals;
  • High clean-up costs and public concern associated with oil spills; and
  • Water Board, California Department of Fish and Game, and U.S. Coast Guard enforcement actions against parties responsible for spills.

The Water Board considered adopting a policy requiring specific improvements in oil transfer operations, but due to the industry's improved performance, the Water Board is holding the adoption of such a policy in abeyance while continuing to monitor the industry's performance. The Water Board recognizes that additional regulation is unnecessary if the petroleum industry maintains its improved record.


Per State Water Board Resolution No. 88-63, almost all the Region's groundwater is considered to be an existing or a potential source of drinking water. With limited resources, the Water Board must concentrate its groundwater protection and management efforts on the most important groundwater basins. DWR has identified 28 individual groundwater basins and seven sub-basins in the Region that serve, or could serve, as sources of high quality drinking water.

Increased demands on these groundwater resources have become evident in the rapidly developing Region. Years of drought and decades of discoveries of groundwater pollution have resulted in impacts or impairment to portions of these basins. Some municipal, domestic, industrial, and agricultural supply wells have been taken out of service due to the presence of pollution. Some of the basins have also been affected by over-pumping, resulting in land subsidence and saltwater intrusion.

Such pressures on groundwater resources require that comprehensive environmental planning and management practices be developed and implemented for each individual basin by all concerned and affected parties. The Water Board will foster this concept with the following groundwater protection and management goals for the Region.

1) Identify and update beneficial uses and water quality objectives for each groundwater basin.

Water quality objectives must maintain the existing high quality of groundwater, protect its beneficial uses, and protect human health and the environment. The Water Board's program to identify and update objectives is described in Section 4.25.1 Application of Water Quality Objectives.

2) Regulate activities that impact or have the potential to impact the beneficial uses of groundwater of the Region.

Federal, state, and local groundwater protection and remediation programs that will result in the overall maintenance or improvement of groundwater quality must be implemented Region-wide in a consistent manner. When a potential threat or problem is discovered, containment and clean-up efforts must be undertaken as quickly as possible to limit groundwater pollution. Where activities that could affect the beneficial uses of groundwater are not regulated by other federal, state, or local programs, the Water Board will consider regulation depending upon the threat to beneficial uses and availability of Water Board resources. The overall requirements for site cleanup and closure, setting cleanup levels, and future groundwater management strategies are described in Section 4.25.2 Requirements for Site Investigation, Cleanup and Site Closure. The Water Board's programs for cleanup of polluted sites are described in Section 4.25.3 Regulation of Potential Pollution Sources.

3) Prevent future impacts to the groundwater resource through local and regional planning, management, education, and monitoring.

Groundwater is an integral component of a watershed's hydrologic system. A comprehensive watershed management approach is necessary to protect groundwater resources. The Water Board's program for broadening its information base on groundwater resources and individual protection needs of basins is described in Section 4.25.4 Groundwater Protection Programs. Groundwater monitoring efforts by state and local agencies are described in Chapter 6 Surveillance and Monitoring.

Local water, fire, planning and health departments are actively involved with their own groundwater protection programs. These programs include: salt water intrusion and land subsidence control, wellhead protection, groundwater recharge area preservation, hazardous material storage and management ordinances, Local Oversight Programs and non-Local Oversight Programs for cleanup of leaking underground fuel tanks, potential conduit well destruction, and well permitting and inspection. For some agencies, maintaining funding for protection programs is an ongoing challenge. Through numerous regional projects, the Water Board is evaluating the groundwater protection needs in specific basins, and thus will provide additional support for local agency efforts.


Water quality objectives apply to all groundwater, rather than at a wellhead or at a point of consumption. The maintenance of the existing high quality of groundwater (i.e., "background") is the primary objective, which defines the lowest concentration limit that the Water Board requires for groundwater protection. The Water Board also has narrative and numeric water quality objectives for bacteria, chemical constituents, radioactivity, and taste and odor (see Chapter 3). These objectives define the upper concentration limit that the Water Board considers protective of beneficial uses. The lower and upper concentration limits define the range that the Water Board considers for clean-up levels of polluted groundwater. Establishment of cleanup levels is discussed in Section 4.25.2 Requirements for Site Investigation, Cleanup and Site Closure.

Numerical limits that implement all applicable water quality objectives include Maximum Contaminant Levels (MCLs) and Secondary Maximum Contaminant Levels (SMCLs), and are only acceptable as the upper end of a concentration range to protect the beneficial uses of municipal and domestic drinking water sources.

Ideally, the Water Board would establish numerical groundwater objectives for all constituents. However, the Water Board is limited in its ability and resources to independently establish numerical objectives for groundwater. To evaluate compliance with water quality objectives, the Water Board will consider all relevant and scientifically valid evidence, including relevant and scientifically valid numerical criteria and guidelines developed and/or published by other agencies and organizations (e.g., State Water Board, U.S. EPA, DHS, Cal/EPA's Office of Environmental Health Hazard Assessment (OEHHA), Cal/EPA's Department of Toxic Substances Control (DTSC), etc.) to provide the numerical criteria for Water Board consideration as groundwater objectives.

The Central Valley Water Board summarized water quality standards and criteria from a variety of sources in “A Compilation of Water Quality Goals”. This report contains an extensive compendium of numerical water quality limits from the literature for over 800 chemical constituents and water quality parameters.

In practice, the Water Board uses water quality objectives for groundwater somewhat differently from those for surface water. For groundwater, the Water Board's emphasis is the regulation of sites where water quality objectives are not being met, clean-up is required and/or under way, and no further waste discharges will be allowed in the future. In contrast, surface water discharges regulated by the Water Board are usually for ongoing discharges regulated to meet water quality objectives in receiving waters.

In a typical situation, the Water Board must identify and establish site- and basin-specific groundwater beneficial uses and standards for the cleanup of groundwater polluted by numerous and extensive spills and leaks of toxic chemicals (e.g., organic solvents, fuels, metals, etc.).

Very few waste discharges to land are allowed by the Water Board and those that are permitted (e.g., landfills, industrial waste disposal, above-ground soil treatment, etc.) are closely regulated under the requirements of existing laws and regulations in order to maintain and protect groundwater quality objectives. An additional category of discharges to land is the numerous individual domestic waste disposal systems (e.g., onsite dispersal systems) that are permitted and regulated by the counties. The Water Board waives regulation based upon the fact that the counties' regulation of the systems complies with applicable Water Board requirements.

Groundwater objectives for individual basins may be developed in the future. As the Water Board completes projects that provide more detailed delineation of beneficial uses within basins, revised objectives may be developed for portions of groundwater basins that have unique protection needs. Examples of Water Board projects completed in the Region are described in "Section 4.25.5 Groundwater Protection Studies.”


This section describes the regulatory requirements and their applications for investigation, cleanup, and closure at sites impacted by soil and groundwater pollution. STATE WATER BOARD POLICIES FOR GROUNDWATER CLEANUP


The “Statement of Policy with Respect to Maintaining High Quality of Waters in California,” known as the Antidegradation Policy (State Water Board Resolution No. 68-16), requires the continued maintenance of existing high quality waters. It provides conditions under which a change in water quality is allowable. A change must:

  • Be consistent with maximum benefit to the people of the state;
  • Not unreasonably affect present and anticipated beneficial uses of water; and
  • Not result in water quality less than that prescribed in water quality control plans or policies.

However, in cases where unauthorized releases have polluted groundwater, restoring groundwater quality to background concentrations is often technically impractical. In those situations, groundwater should be restored to attain applicable beneficial uses.


This policy, adopted by the State Water Board in 1988 (Resolution No. 88-63), established state policy that all surface and ground water in the state are considered suitable, or potentially suitable, for municipal or domestic supply (MUN) and should be designated for this use, with certain exceptions. The exceptions for groundwater are:

  • The groundwater’s TDS exceeds 3,000 mg/L (5,000 microSiemens per centimeter (μS/cm), electrical conductivity), and it is not reasonably expected by the Water Boards to supply a public water system; or
  • There is contamination, either by natural processes or by human activity (unrelated to the specific pollution incident), that cannot reasonably be treated for domestic use through implementation of BMPs or best economically achievable treatment practices; or
  • The water source does not provide sufficient water to supply a single well capable of producing an average, sustained yield of 200 gallons per day; or
  • The aquifer is regulated as a geothermal energy-producing source or has been exempted administratively pursuant to 40 Code of Federal Regulations (CFR), Section 146.4 for the purpose of underground injection of fluids associated with the production of hydrocarbon or geothermal energy, provided that these fluids do not constitute a hazardous waste under 40 CFR, Section 261.3.


State Water Board Resolution No. 92-49, "Policies and Procedures for Investigation, Cleanup and Abatement of Discharges Under Water Code Section 13304" contains the policies and procedures that all Water Boards shall follow to oversee and regulate investigations and cleanup and abatement activities resulting from all types of discharge or threat of discharge subject to Water Code Section 13304. Therefore, the five program areas described below follow the same policies and procedures outlined in Resolution No. 92-49 for determining:

  • When an investigation is required;
  • The scope of phased investigations necessary to define the nature and extent of contamination or pollution;
  • Cost-effective procedures to detect, cleanup or abate contamination; and
  • Reasonable schedules for investigation, cleanup, abatement, or any other remedial action at a site.

State Water Board Resolution No. 92-49 requires that the Water Board ensure that the discharger is aware of and considers minimum cleanup and abatement methods. The minimum methods that the discharger should be aware of and consider, to the extent that they may be applicable to the discharge or threat thereof, are:

  • Source removal and/or isolation;
  • In-place treatment of soil or water, including bioremediation, aeration, and fixation;
  • Excavation or extraction of soil, water, or gas for on-site or off-site treatment techniques including bioremediation; thermal destruction; aeration; sorption; precipitation, flocculation and sedimentation; filtration; fixation; and evaporation; and,
  • Excavation or extraction of soil, water, or gas for appropriate recycling, reuse, or disposal.

State Water Board Resolution No. 92-49 was amended in 1996 with Resolution No. 96-79, Containment Zone Policy. Per the revised resolution, it is not the intent of the State Water Board or the Regional Water Boards to allow dischargers, whose actions have caused, permitted, or threaten to cause or permit conditions of pollution, to avoid responsibilities for cleanup. However, in some cases, attainment of applicable water quality objectives for groundwater cannot reasonably be achieved. In these cases, the State Water Board determines that establishment of a containment zone is appropriate and consistent with the maximum benefit to the people of the state if applicable requirements contained in the policy are satisfied.


In addition to State Water Board policies that specify requirements for investigation and cleanup of groundwater, State Water Board precedential orders on petitions provide guidance and direction to the nine Regional Water Boards with respect to cleanup orders. State Water Board decisions affecting site cleanup fall into three general categories: naming responsible parties, setting cleanup standards, and closing low-risk cases. ELEMENTS OF GROUNDWATER CLEANUP AND SITE CLOSURE

State Water Board Resolution No. 92-49 outlines the five basic elements of a site investigation. Any or all elements of an investigation may proceed concurrently, rather than sequentially, in order to expedite cleanup and abatement of a discharge, provided that the overall cleanup goals and abatement are not compromised. State Water Board Resolution No. 92-49 investigation components are as follows:

  1. Preliminary site assessment to confirm the discharge and the identity of the dischargers; to identify affected or threatened waters of the state and their beneficial uses; and to develop preliminary information on the nature and vertical and horizontal extent, of the discharge;
  2. Soil and water investigation to determine the source, nature, and extent of the discharge with sufficient detail to provide the basis for decisions regarding subsequent clean-up and abatement actions, if any are determined by the Regional Water Board to be necessary;
  3. Proposal and selection of clean-up action to evaluate feasible and effective cleanup and abatement actions and to develop preferred clean-up and abatement alternatives;
  4. Implementation of clean-up and abatement action to implement the selected alternative and to monitor in order to verify progress; and
  5. Monitoring to confirm short- and long-term effectiveness of cleanup and abatement.

The following additional requirements for site cleanup and closure may also apply, as described below.

“Cleanup Complete” Determinations – The Water Board provides no further action (NFA) confirmations and no-further-active-cleanup confirmations to responsible parties when no further active cleanup is needed. For petroleum-impacted sites, the Water Board provides a case closure letter as part of the case closure summary report.

Public Participation – The Water Board will provide opportunities for public participation in the oversight process so that the public is informed and has the opportunity to comment. The level of effort is tailored to site-specific conditions, depending on site complexity and public interest. The level of public participation effort at a particular site is based on the potential threat to human health, water quality, and the environment; the degree of public concern or interest in site cleanup; and any environmental justice factors associated with the site.

Electronic Data Reporting – The State Water Board maintains a web-based geographic information system (GIS) program that provides the public and regulators with online access to environmental data. The State Water Board adopted regulations that require electronic submittal of information for groundwater cleanup programs (Title 23, CCR, Division 3, Chapter 30). For several years, parties responsible for cleanup of leaking underground fuel tanks (LUFT) have been required to submit groundwater analytical data, the surveyed locations of monitoring wells, and certain other data to the State Water Board database over the Internet. As of 2005, all groundwater cleanup programs are required to submit these items as well as a portable data format (PDF) copy of reports.

Compliance Monitoring – Monitoring reports are required periodically that describe the status of the cleanup activities and monitoring results. The Water Board will conduct site inspections to ensure the responsible party is complying with Water Board enforcement directives.

Deed Restriction - A deed restriction (land use covenant) may be required to facilitate the remediation of past environmental contamination and to protect human health and the environment by reducing the risk of exposure to residual hazardous materials. Water Code Section 13307.1 requires that deed restrictions be mandated for sites that are not cleaned up to “unrestricted use”, and that the restrictions be recorded and run with the land to prohibit sensitive uses such as homes, schools, or day care facilities. Underground storage tank (UST) sites are exempted from this requirement because of the sheer numbers and the small size of most of these sites. Site conditions are tracked in the statewide database developed by the State Water Board (Section Electronic Data Reporting).

Liability Relief Tools – Several tools are available to municipalities, landowners, developers and responsible parties for seeking relief from contamination liability. The Polanco Act, California Land Environmental Restoration and Reuse Act, and California Land Reuse and Revitalization Act provide liability relief and help redevelopment agencies, cities and counties to guide and pursue redevelopment of Brownfield sites (Section Brownfields). SETTING CLEANUP LEVELS

The Water Board approves soil and groundwater clean-up levels for polluted sites. Per State Board Resolution No. 92-49, the basis for Water Board decisions regarding investigation, and cleanup and abatement includes: (1) site-specific characteristics; (2) applicable state and federal statutes and regulations; (3) applicable water quality control plans adopted by the State and Regional Water Boards, including beneficial uses, water quality objectives, and implementation plans; (4) State and Regional Water Board policies, including State Water Board Resolutions No. 68-16 (Antidegradation Policy) and No. 88-63 (Sources of Drinking Water Policy); and (5) relevant standards, criteria, and advisories adopted by other state and federal agencies.

State Water Board Resolution No. 92-49 directs the Regional Water Boards to ensure that dischargers are required to cleanup and abate the effect of discharges. This cleanup and abatement shall be done in a manner that promotes attainment of either background water quality, or the best water quality that is reasonable if background levels of water quality cannot be restored, considering all demands being made and to be made on those waters and the total values involved: beneficial and detrimental, economic and social, tangible and intangible. Any alternative cleanup levels less stringent than background shall:

  • Be consistent with maximum benefit to the people of the state;
  • Not unreasonably affect present and anticipated beneficial uses of such water; and
  • Not result in water quality less than that prescribed in the Water Quality Control Plans and Policies adopted by the State and Regional Water Boards.

The overall clean-up level established for a waterbody is based upon the most sensitive beneficial use identified. In all cases, the Water Board first considers high quality or naturally occurring "background" concentration objectives as the clean-up levels for polluted groundwater and the factors listed above under "Setting Cleanup Levels." For groundwaters with a beneficial use of municipal and domestic supply, cleanup levels are set no higher than:

  • MCLs or adopted SMCLs, whichever is more restrictive, or
  • A more stringent level (i.e., below MCLs) based upon a site-specific risk assessment. Clean-up levels must be set to maintain the excess upperbound lifetime cancer risk to an individual of less than 1 in 10,000 (10-4) or a cumulative toxicological effect as measured by the Hazard Index of less than one. For all sites performing risk assessments, an alternative with an excess cancer risk of 1 in 1,000,000 (10-6) or less must also be considered.

The Water Board determines excess cancer risks and the Hazard Index following the procedures described in the U.S. EPA's Risk Assessment Guidance for Superfund, Volume I, Parts A dated August 1989, B dated December 1991, and C dated December 1991, which are incorporated by reference into this plan. The Water Board may modify the U.S. EPA's approach based on OEHHA's guidelines or more current site- or pollutant-specific information.

Groundwater clean-up levels are approved on a case-by-case basis by the Water Board. The Executive Officer or a local agency may approve clean-up levels as appropriately established by the Water Board. Proposed final clean-up levels are based on a discharger-developed feasibility study of clean-up alternatives that compares effectiveness, cost, time to achieve clean-up standards, and a risk assessment to determine impacts on beneficial uses, human health, and the environment. Clean-up levels must also take into account the mobility, toxicity, and volume of pollutants. Feasibility studies of cleanup alternatives may include the guidance provided by Subpart E of the National Oil and Hazardous Substances Pollution Contingency Plan (40 CFR 300); Section 25356.1(c) of the California Health and Safety Code; CERCLA; the State Water Board's Resolutions Nos. 68-16 and 92-49; and the Water Board Resolution No. 88-160.


Soil pollution can present a health risk and a threat to water quality. The Water Board sets soil clean-up levels for the unsaturated zone based on these threats. Guidance from the U.S. EPA, DTSC, and OEHHA are considered when determining cleanup levels. Cleanup levels must be protective of human health for existing and likely future land use based on properly adopted land use designations in general plans, zoning, and other mechanisms. In addition, if it is unreasonable to cleanup soils to background concentration levels, the Water Board may:

  • Allow residual pollutants to remain in soil at concentrations such that:

    a) Any residual mobile constituents generated would not cause groundwater to exceed applicable groundwater quality objectives, and

    b) Health risks from surface or subsurface exposure are within acceptable guidelines.

  • Require follow-up groundwater monitoring to verify that groundwater is not polluted by chemicals remaining in the soil. Follow-up groundwater monitoring may not be required where residual soil pollutants are not expected to impact groundwater.
  • Require measures to ensure that soils with residual pollutants are covered and managed to minimize pollution of surface waters and/or exposure to the public.
  • Implement applicable provisions of CCR Title 27 where significant amounts of wastes remain on-site. This may include, but is not limited to, subsurface barriers, pollutant immobilization, toxicity reduction, and financial assurances.

In order for a discharger to make site-specific recommendations for soil clean-up levels above background, the fate and transport of leachate can be modeled by the discharger using site-specific factors and appropriate models. Assumptions for minimal leachate dilution, as proposed by the discharger, may be considered by the Water Board if deemed reasonable.


Sites with identified pollution problems are managed through five program areas: (1) Spills, Leaks, Investigations, and Cleanups (SLIC) Program; (2) UST Program; (3) Landfill Program, (4) Department of Defense/Department of Energy (DoD/DoE) Program and (5) Above-ground Petroleum Storage Tank Program. Requirements for site investigation and remediation of groundwater under these programs are described in Section 4.25.2 Requirements for Site Investigation, Cleanup, and Site Closure. SPILLS, LEAKS, INVESTIGATION, AND CLEANUP PROGRAM (SLIC)

The SLIC program focuses on unauthorized releases of pollutants to soil, surface water, and groundwater. Sites that are managed within the SLIC program include sites with pollution from recent or historical surface spills, subsurface releases (e.g., pipelines, sumps, etc.), and all other unauthorized discharges that pollute or threaten to pollute surface or groundwater. The SLIC program also includes groundwater cleanup at Brownfields, refineries, and other large industrial facilities. There is some overlap with the UST program as many SLIC cases also have leaking underground tanks.

The Water Board identified many historical releases in the 1980s. New releases are identified through discharger reports, complaints to the Water Board, the Water Board's own surveillance, “due diligence” reports for proposed property transfer or redevelopment, and local agency reports.

There are variety of different pollutants at SLIC sites, including chlorinated solvents, fuels and non-chlorinated solvents, SVOCs, inorganic constituents and metals, polychlorinated biphenols (PCBs), and pesticides. Persistent and mobile constituents, such as chlorinated solvents, tend to cause more serious pollution problems, while immobile constituents, such as metals, and biodegradable constituents, such as fuels, tend to be less serious. Two other factors can increase case complexity: multiple dischargers on a site (such as a current owner, past owner, and past operator) and commingled groundwater plumes, where contaminants from two or more source sites have merged. In both cases, dischargers may argue against being named in cleanup orders or may demand that other parties be named as well.

The Water Code provides authority for the Water Board to require investigation and cleanup of sites with unauthorized pollutant releases. Water Code Section 13267 allows the Water Board to require technical reports from suspected dischargers. Water Code Section 13304 authorizes the Water Board to issue “cleanup and abatement” orders requiring a discharger to cleanup and abate waste, “where the discharger has caused or permitted waste to be discharged or deposited where it is or probably will be discharged into waters of the State and creates or threatens to create a condition of pollution or nuisance.” The Water Board coined the term “site cleanup requirements” (SCRs) to describe Water Code Section 13304 orders where soil or groundwater cleanup would take many years to complete and the dischargers are cooperating.

The Water Board also complies with any requirements in the state Health and Safety Code and the federal Superfund law for authority at federal Superfund sites where the Water Board is the lead agency.


Water Code Section 13304 authorizes the Regional Water Boards to recover costs for oversight of site cleanup at sites where a discharge of waste has occurred and that discharge creates, or threatens to create, a condition of pollution or nuisance. The Water Board was instrumental in establishing the State Water Board’s SLIC cost recovery program. Cost recovery was initially established in the early 1990s with the agreement of Bay Area petroleum refineries to reimburse the state for oversight of groundwater and soil remediation. Shortly thereafter the State Water Board organized a pilot program to expand the cost recovery program to other SLIC sites. During this period the legislature amended this section of the Water Code to strengthen the ability of the Regional Water Boards to recover staff oversight costs.

In 1993, the State Water Board established a unified SLIC cost recovery program. Program funding came initially from the General Fund but later switched to the State Water Board’s Cleanup and Abatement Account (revolving fund mechanism). The net cost of this program to the state is a small fraction of this amount because dischargers repay almost all of the staff oversight costs.

In general, SLIC sites should be enrolled in the SLIC cost recovery program because there is very limited program funding for oversight of non-cost recovery sites. Exceptions include de minimus sites (e.g., sites where oversight can be completed with minimal staff effort), and under special circumstances (e.g., sites with significant potential threat to human health or water quality where there are limited funds available for remedial action).


Superfund Sites – The federal Superfund program was created in 1980 when Congress enacted CERCLA, known as Superfund. CERCLA was amended in 1986 with the Superfund Amendments and Reauthorization Act (SARA). The Water Board is the lead regulatory oversight agency for 16 federal Superfund sites in the South Bay. The Superfund program was designed to address the most seriously contaminated hazardous waste sites in the country. The Water Board previously had a U.S. EPA grant to oversee the 16 federal Superfund sites. Currently the sites are all enrolled in the Water Board's cost recovery program and are managed similar to SLIC cases while still ensuring that U.S. EPA's requirements, as defined in the National Contingency Plan, are met. The Water Board has adopted final SCRs for all 16 sites, and all 16 sites have implemented long-term remediation projects.

RCRA Sites – Six sites originally proposed as federal Superfund sites were subsequently dropped because cleanup could be required under Resource Conservation and Recovery Act (RCRA). As with the Superfund sites, the Water Board has adopted final SCRs for all sites in compliance with RCRA requirements, and all six sites have implemented long-term remediation projects. There are also about 20 RCRA “analogous” sites. These are sites where Water Board oversight has included extra steps to assure that oversight is analogous to the state and federal RCRA requirements. The Water Board has adopted SCRs for all “analogous” sites, and most have implemented long-term remediation.


The Water Board is one of several agencies with a role in the Brownfield cleanup and redevelopment process. Brownfields are properties that are contaminated, or thought to be contaminated, and are underutilized due to perceived remediation costs and liability concerns. The Water Board directly oversees investigation and cleanup at Brownfield sites. Other stakeholders in the process include: local redevelopment agencies (who designate redevelopment areas and often acquire and assist in redevelop of Brownfield sites), local governments (who must approve redevelopment proposals), developers and non-profits (who make redevelopment proposals), lenders, and community members.


There are several key federal and state environmental laws that have fostered Brownfield development, as described below.

Federal Legislation

The Small Business Liability Relief and Brownfields Revitalization Act (Brownfield Law) signed into law in 2002 contains three subtitles dealing with funding and liability for assessing and cleaning up contaminated properties. Subtitle A codified and expanded U.S. EPA’s current Brownfield program by authorizing funding for assessment and cleanup of Brownfield sites. Subtitle B exempted contiguous property owners and prospective purchasers from Superfund liability, and clarified the extent of appropriate environmental inquiry for innocent landowners. “Innocent landowners” are those who hold property with contamination on it, but did not contribute to the pollution. Subtitle C authorized funding for State response programs and limited U.S. EPA’s Superfund enforcement authority at sites cleaned up under a State response program.

This law is important because it provides liability relief for innocent landowners and purchasers as long as they meet certain requirements. Many redevelopment deals have stalled previously because there was no clear-cut mechanism for providing liability relief to innocent purchasers who were willing to perform the cleanup, but unwilling to take on the long-term liability associated with the site.

State Legislation

The Polanco Redevelopment Act of 1990 (Polanco) outlines the processes for redevelopment agencies to follow when cleaning up a hazardous substance release in a redevelopment project area. It also provides immunity from liability for redevelopment agencies and subsequent property purchasers for sites cleaned up under a plan approved by the Water Board (or DTSC). The Polanco process has become a widely used tool by redevelopment agencies to guide and pursue redevelopment of Brownfields. Redevelopment agencies requesting approval of their cleanup plans under the provisions of Polanco are required to reimburse oversight costs to the agencies.

The California Land Environmental Restoration and Reuse Act of 2001 was enacted to enable cities and counties to direct or conduct investigation and remediation at Brownfield sites that are outside of redevelopment areas to help return Brownfields to productive uses. It requires Cal/EPA to provide a variety of data related to Brownfield cleanups, and to develop a set of screening values for hazardous substances commonly found at Brownfield sites. A centerpiece of the legislation was its requirement that Cal/EPA develop statewide screening levels, based on environmental screening levels developed at this Water Board (Section Setting Cleanup Levels).

The California Land Reuse and Revitalization Act of 2004 (CLRRA) is intended to bring California into conformity with the federal statutes concerning liability relief for innocent landowners, perspective (bona fide) purchasers, and contiguous property owners in urban areas. It allows for risk-based cleanups at Brownfield sites. Participants who seek immunity must enter into an agreement with the agency that includes the preparation and implementation of a site assessment plan, and if necessary, a response plan. A certificate of completion is issued upon determining that all response actions have been completed in accordance with the agency approval process.


Brownfield Grants

The U.S. EPA provides two types of Brownfield grants to states for the purpose of promoting Brownfield redevelopment, and to local agencies and non-profits to jump-start specific Brownfield redevelopment projects. The Water Board has worked closely with several cities in the Region to encourage Brownfield site cleanup and redevelopment, including writing letters of support for project-specific U.S. EPA grants. Between 1996 and 2005, U.S. EPA has awarded Brownfield grants totaling $9 million within the Region. The City of Oakland alone has received over $2 million in grants. Other recipient jurisdictions include: Emeryville, East Palo Alto, Richmond, San Francisco, Livermore, Alameda County, Contra Costa County, San Pablo, Petaluma, San Jose, and Union City.

Cal/EPA’s Brownfield Initiative

In 2004, Cal/EPA announced a Brownfield initiative aimed at improving the way Cal/EPA agencies coordinate their regulatory activities at Brownfield sites. The initiative includes an ambitious implementation plan to:

  • Foster partnerships with Brownfield stakeholders;
  • Develop an inventory of Brownfield sites in California;
  • Provide liability relief to Brownfield owners and buyers; and
  • Pursue necessary funding and resources for Brownfield cleanup.

The initiative also directed the State Water Board, Regional Water Boards, and DTSC to complete a MOA. The MOA was signed in 2005 and contains the following elements:

  • Limit oversight to a single lead agency at any given site;
  • Establish procedures for identifying the appropriate lead agency;
  • Establish a uniform site assessment procedure to be used by both agencies;
  • Require that cleanups address the issues and concerns of both agencies;
  • Allow the lead agency to gain the advice and expertise of the other agency as appropriate;
  • Ensure ample opportunities for public input and involvement;
  • Establish target timeframes for completing investigation and cleanup; and
  • Establish regular coordinating meetings.

California State Liability Relief Tools

Several tools are available to municipalities, landowners, developers and responsible parties for seeking relief from contamination liability. Polanco, the California Land Environmental Restoration and Reuse Act, and CLLRA provide liability relief and help redevelopment agencies, cities and counties to guide and pursue redevelopment of Brownfields. Prospective purchaser agreements (PPA) are agreements to protect purchasers from being named as a discharger for pre-existing pollution. The buyer must provide something in return, such as an agreement to provide reasonable access for site cleanup and monitoring.

The Water Board may issue “comfort letters” to buyers of polluted property or owners of off-site properties affected by migrating groundwater pollution to mollify buyers or lenders about the potential liability they face. Letters to offsite owners typically promise not to enforce against them as long as they provide reasonable access. Letters to onsite buyers typically promise not to enforce against them as long as they provide reasonable access and the current responsible parties continue to perform necessary cleanup work. UNDERGROUND STORAGE TANK PROGRAM

A UST is defined by law as "any one or combination of tanks, including pipes connected thereto, that is used for the storage of hazardous substances and that is substantially or totally beneath the surface of the ground" (certain exceptions apply). The purpose of the UST Program is to protect public health and safety and the environment from releases of petroleum and other hazardous substances from tanks. State regulations regarding underground tank construction, monitoring, repair, closure, release reporting, and corrective action are contained within CCR Title 23, Chapter 16.

Implementation of the UST Program is unique, as the Health and Safety Code Division 20, Chapters 6.7 and 6.75, gives local agencies the authority to oversee investigation and cleanup of UST leak sites. The Corrective Action regulations (CCR, Title 23, Chapter 16, Article 11) use the term "regulatory agency" in recognition of the fact that local agencies have the option to oversee site investigation and cleanup, in addition to their statutory mandate to oversee leak reporting and tank closure.

Some local agencies also provide oversight for underground fuel storage tank cases under a Local Oversight Program (LOP) contract with the State Water Board. Most oversight charges are billed to responsible parties. Some LOPs, known as Local Implementing Agencies (LIAs), have independent authority under UST laws to require investigations and cleanup. The Water Board still retains its Water Code authority to approve case closure. However, the Water Board has authorized a few local agencies to close fuel leak cases where groundwater has not been polluted, and future groundwater impacts are not expected.

Additionally, a few other local agencies have funded their own (non-LOP) oversight programs and have developed guidance documents based upon State and Regional Water Board guidance. In many areas throughout the Region the local agency has opted not to assume the lead position for fuel leak cases. Consequently, the Water Board is the lead agency for fuel leak sites in those areas.


Certified Unified Permitting Agencies (CUPAs) permit and regulate UST operations including leak prevention and inspections. When a release occurs, the Water Board is generally notified of the release via a copy of an Unauthorized Release Form (URF). This form is tailored so as its notification hierarchy complies with Proposition 65 notification requirements.

If the release is fuel based, and the CUPA happens to also be an LOP agency or an agency that has an agreement with the Water Board for fuel UST cleanup oversight, it will oversee cleanup operations from that point. All of this Region’s LOP agencies are part of a CUPA. The same holds true in the case of our LIA agencies, with the exception of the Alameda County Water District (ACWD).

If the release is solvent based, the Water Board will provide oversight for cleanup. Exceptions may be found for those situations for which DTSC is the lead agency because the tank is on a site that is under DTSC lead, such as the solvent UST being located within a RCRA site, or by mutual agency agreement.


The Water Board oversees cases for all of Contra Costa County, Marin County, and various cases within the LOP and LIA jurisdictions.

The Water Board having the lead in UST cases is the result of one or more of the following: 1) solvents or solvents commingled with fuels are the pollutant of concern; 2) the petroleum discharge is from something other than a UST under the Local Oversight Program or not necessarily under UST regulation such as sumps, spills, or agricultural tanks; 3) complex technical or policy issues; 4) conflict of interest issues in which the local agency is the responsible party, there is inappropriate political pressure on the case, or for which the agency requests Water Board lead; 5) cases given to the Water Board as part of the Site Designation Process (AB 2061); 6) the local agency is unable, unwilling, and/or unavailable to provide proper oversight; 7) part of the site is within a larger facility currently under Water Board oversight; and 8) historical precedent.

Local Oversight Program (LOP) Agencies

Although the LOP agency contracts with the State Water Board, the Water Board provides technical guidance and enforcement support as needed. Upon determination by the LOP agency that a case is ready for closure, the LOP agency submits a closure package to Water Board for review. If the Water Board concurs or fails to act within 30 days, the closure is deemed approved and the LOP agency issues the closure letter.

The following agencies are LOPs in the Region, as of 2005:

  • Alameda County Health Care Services, Department of Environmental Health
  • Napa County Department of Environmental Management
  • San Francisco Department of Public Health, Bureau of Environmental Health Management
  • San Mateo County Department of Health Services, Office of Environmental Health
  • Santa Clara County Department of Environmental Health
  • Solano County Department of Environmental Management
  • Sonoma County Department of Health Services, Environmental Health Division

Local Implementing Agencies (LIAs)

The Water Board provides technical and enforcement assistance to the LIAs, as necessary. However, these agencies essentially perform the same technical oversight duties (report requests, report review, etc.) that the Water Board would be expected to perform when overseeing case cleanups.

As part of this Region’s case closure protocol with the LIA agencies, the Water Board reviews the LIA’s case closure recommendation and case closure summary package (although in some cases the Water Board may prepare the summary package for the agency). If the Water Board concurs with the agency’s recommendation, the Water Board issues the closure letter.

The following agencies are LIAs in the Region, as of 2005:

  • Alameda County Water District
  • City of Berkeley Toxics Management Program
  • City of Hayward Fire Department
  • City of San Leandro


In 1995, the State Water Board commissioned the Lawrence Livermore National Laboratory (LLNL) and the University of California to conduct a review of the regulatory framework and cleanup process applied to LUFTs. The study titled, “Recommendations to Improve the Cleanup Process for California’s Leaking Underground Fuel Tanks (LUFTs)” concluded that fuel hydrocarbons have limited impact on human health, the environment, or California's groundwater resources, and recommended applying a modified ASTM risk-based corrective action (RBCA) process for closing leaking UST sites (ASTM E1739-95, 2002). A risk-based approach to leaking UST cleanups has been widely applied following this recommendation.

In the mid 1990's, methyl tert-butyl ether (MtBE) was recognized as a major threat to groundwater resources. MtBE had been added to gasoline sold in California since 1979 until January 1, 2004, first as an octane booster, and later as an oxygenate comprising up to 11 percent by volume. MtBE prioritization guidelines were developed based on a risk-based approach, and the expedited site assessment has been used to cleanup high threat MtBE sites (Expedited Site Assessment Tools for UST Sites (EPA 510-B-97-001, 1997)).

In 1998, the State Water Board commissioned LLNL to study the impacts of MtBE on groundwater in California. LLNL concluded that MtBE is a frequent and widespread contaminant in shallow groundwater throughout California and that MtBE plumes are more mobile than benzene, toluene, ethylbenzene, and xylenes (BTEX) plumes (An Evaluation of MTBE Impacts to California Groundwater Resources, 1998). Guidelines were developed by the State Water Board for investigation and cleanup of MtBE and other ether-based oxygenates (Guidelines for Investigation and Cleanup of MtBE and Other Ether-Based Oxygenates, 2001).

Since 1998 several studies have been conducted that evaluated the occurrence of MtBE releases at UST sites. These studies indicated that effectiveness of the existing UST leak detection systems has been limited, and that MtBE has impacted the majority of the UST sites (Report on MtBE Monitoring at Operating UST Facilities in Santa Clara County, 2004).


Federal and state laws require every owner and operator of a petroleum UST to maintain financial responsibility to pay for any damages arising from their tank operations. The Barry Keene Underground Storage Tank Cleanup Fund Act of 1989 (Cleanup Fund) was created by the California Legislature, and is administered by the State Water Board, to provide a means for petroleum UST owners and operators to meet the federal and state requirements. The Cleanup Fund also assists a large number of small businesses and individuals by providing reimbursement for unexpected and catastrophic expenses associated with the cleanup of leaking petroleum USTs.

If a leak occurs, responsible parties or their representative must notify the appropriate Water Board or county agency and submit an unauthorized release form (URF). The Cleanup Fund can only reimburse costs after the site investigation and cleanup of the tank release has been reported to the Water Board or county regulatory agency. LANDFILL PROGRAM

Discharges of solid, semisolid, and liquid wastes to landfills, waste piles, surface impoundments, and land treatment facilities can create sources of pollution affecting the quality of waters of the state. Low-concentration liquid waste discharges can be assimilated by receiving waters, if the concentration of pollutants in the waste is regulated (i.e., treated wastewater from municipal or industrial facilities). Conversely, discharges of wastes to waste management units require long-term containment or active treatment in order to prevent waste or waste constituents from migrating to and impairing the beneficial uses of waters of the state. Pollutants from such discharges may continue to affect water quality long after the discharger has stopped discharging new wastes at a site, either because of undetermined releases from the site or because pollutants from the site have accumulated in underlying soils and are migrating to groundwater.

Landfills for disposal of municipal or industrial solid waste (solid waste disposal sites) are the major categories of waste management units located in the Region. The Water Board issues WDRs to ensure that these discharges are properly contained to protect the Region's water resources from degradation and to ensure that the dischargers undertake effective monitoring to verify continued compliance with requirements.

These discharges, and the waste management units at which the wastes are discharged, are subject to concurrent regulation by other state and local agencies responsible for land-use planning, solid waste management, and hazardous waste management. Local enforcement agencies (LEAs) implement the state's solid waste management laws and local ordinances governing the siting, design, and operation of solid waste disposal facilities (usually landfills) with the concurrence of the California Integrated Waste Management Board (CIWMB). The CIWMB also has direct responsibility for review and approval of plans for closure and post-closure maintenance of solid waste landfills. DTSC issues permits for all hazardous waste. The State Water Board, Regional Water Boards, the CIWMB, and DTSC have entered into a Memorandum of Understanding to coordinate their respective roles in the concurrent regulation of these discharges.

Oversight costs for sites in the landfill program at the Water Board and CIWMB are primarily funded through waste discharge permit fees and landfill waste tipping fees.

The Water Board regulates landfills receiving municipal solid wastes (MSW) and facilities receiving classified, nonhazardous, and industrial wastes of various types. Figure 4-6 shows the active and inactive municipal solid waste landfill sites within the Region as of 2005. The Water Board regulates these sites closely, but the required monitoring has revealed water quality problems at some sites that the respective owners or operators are addressing through appropriate remedial measures. As a result of federal laws in the area of hazardous waste regulation, more effort is being devoted to regulation of the onsite treatment, storage, and disposal of hazardous waste.


In 1997, the State revised and strengthened the laws and regulations governing the discharges of both hazardous and nonhazardous solid waste. The primary purpose of the regulations is to: 1) assure the protection of human health and the environment, 2) ensure waste is properly contained or cleaned-up as appropriate, and 3) protect surface water and groundwater from the discharge of waste to land. The primary regulation used by the Water Board in regulating nonhazardous waste treatment, storage, and disposal is the combined State Water Board and CIWMB regulations contained in `CCR Title 27, Division 2 of the Solid Waste Regulations, formerly CCR Title 23, Division 3, Chapter 15. Title 27 includes very specific siting, construction, monitoring, and closure requirements for all existing and new nonhazardous waste treatment, storage, and disposal facilities. Title 27 also contains a provision requiring operators to provide assurances of financial responsibility for: landfill closure activities; post closure monitoring and maintenance; and corrective action for landfill releases. Title 27 establishes detailed technical criteria for establishing water quality protection standards, monitoring programs, and corrective action programs for releases from waste management units.

Title 27 defines three types of nonhazardous waste: 1) designated wastes; 2) nonhazardous solid waste; and 3) inert waste, as described below.

Unlike other waste classifications, designated waste is defined in Water Code Section 13173 (and in Title 27) as follows:

"Designated waste,” means either of the following:

  1. Hazardous waste that has been granted a variance from hazardous waste management requirements pursuant to Section 25143 of the Health and Safety Code-.
  2. Nonhazardous waste that consists of, or contains, pollutants that, under ambient environmental conditions at a waste management unit, could be released in concentrations exceeding applicable water quality objectives or that could reasonably be expected to affect beneficial uses of the waters of the state as contained in the appropriate state water quality control plan.

Title 27 Section 20220 defines nonhazardous solid waste as waste normally associated with domestic, agricultural, and commercial activities. In addition to the regulations under Title 27, landfills that receive nonhazardous solid waste are subject to the State Water Board’s special regulations for municipal solid waste landfills (State Water Board Resolution No. 93-62), which adapt federal municipal solid waste landfill standards to the state’s landfill regulation scheme.

Title 27 Section 20230 defines inert waste as that subset of nonhazardous solid waste that does not contain hazardous waste or soluble pollutants at concentrations in excess of applicable water quality objectives, and does not contain significant quantities of decomposable waste. The Water Board regulates inert waste landfills outside of its Title 27 authority and only to the extent necessary to protect water quality from siltation and other indirect effects.

The Water Board regulates discharges of designated waste and nonhazardous solid waste pursuant to the regulations in Title 27; regulates discharges of municipal solid waste pursuant to both the Title 27 regulations and State Water Board Resolution No. 93-62; and regulates discharges of inert wastes only as necessary to protect water quality (e.g., to prevent sediment discharges to surface waters or to assure that such relatively unregulated units receive only inert waste).

Hazardous waste is defined by DTSC in CCR Title 22, Division 4.5, Chapter 11. Disposal of hazardous waste and hazardous waste sites located in the Region are regulated by DTSC.

The Water Board has been regulating nonhazardous solid waste facilities since the mid-1970's, and in some instances since to the early 1950's. Many of the small, older facilities have closed, and waste is now being disposed of at large regional nonhazardous solid waste facilities. The Water Board reviews and revises WDRs at active nonhazardous waste sites, and at closed sites, and assures consistency with the current regulations. These actions include defining the levels of designated wastes (see below), requiring the discharger to establish and operate groundwater monitoring systems capable of identifying whether water quality objectives are being violated, establishing corrective evaluation monitoring (investigation) and corrective action programs where standards are violated, and reviewing and overseeing the development and implementation of facility closure plans. Active landfills are also subject to construction and industrial stormwater NPDES permit requirements (Section 4.14 Urban Runoff Management).

To implement Title 27 at nonhazardous solid waste facilities, the Water Board must define designated wastes. Many wastes which are not hazardous still contain constituents of water quality concern that could become soluble in a nonhazardous solid waste facility and produce leachates and gases that could pose a threat to beneficial uses of state waters. Furthermore, a waste (e.g., salty solids) that might be a designated waste at a landfill that overlies potable water would not be a designated waste at one that overlies groundwater with non-potable water at comparable concentrations (i.e., salty solids are not a threat to salty groundwater).

The criteria for determining if a nonhazardous waste is a designated waste are based on water quality objectives in the vicinity of the site, the containment features of the solid waste facility, and the solubility/mobility of the waste constituents. Therefore, all owners and operators of active nonhazardous municipal solid waste facilities in the Region who wish to receive wastes other than municipal solid waste or inert wastes must propose waste constituent concentration criteria above which wastes will be considered designated waste and therefore, not suitable for disposal at their site. In determining whether a nonhazardous waste is designated waste, the Water Board will consider all relevant and scientifically valid evidence, including relevant and scientifically valid numerical criteria and guidelines developed and/or published by other sources, such as the Central Valley Water Board's report, "Designated Level Methodology for Waste Classification and Cleanup Level Determination," or an equivalent methodology acceptable to the Executive Officer.


The state implements federally authorized regulations that are equivalent to those promulgated by the U.S. EPA under Subtitle C of RCRA -- Hazardous Waste Regulations for Treatment, Storage, and Disposal. In 1992, U.S. EPA formally delegated RCRA Subtitle C program implementation authority to DTSC. As described above, regulation of hazardous waste discharges is also included in CCR Title 23, Chapter 15. Chapter 15 monitoring requirements were amended in 1997 to be equivalent to RCRA requirements in regard to the discharge of hazardous waste to land.

The U.S. EPA promulgated federal regulations, as required by Subtitle D of the federal RCRA statute, applicable to municipal solid waste landfills (40 CFR 257 and 258). These regulations are self-implementing. The CIWMB and the State Water Board are jointly responsible for implementing the state program, which the U.S. EPA has approved as being equivalent. The Regional Water Boards implement the water quality aspects of the state program. The LEAs and the CIWMB implement the public health and safety aspects of the state program.


The Toxic Pits Cleanup Act of 1984 (TPCA) required that all impoundments containing liquid hazardous wastes or free liquids containing hazardous waste be retrofitted with a liner/leachate collection system or be dried out by July 1, 1988, and subsequently closed. In 1985, there were 26 sites in the Region with ponds subject to TPCA. As of 2005, one site is permitted to operate its ponds under TPCA's exemption requirement but is not accepting waste and is seeking closure. The remaining 25 sites have been closed.


A significant issue that the Water Board has addressed is the expansion of existing Bayfront landfills into wetland areas. The Water Board, in a few cases, allowed modest expansions (and undesirable loss of wetlands) to allow local governments time to develop other disposal options. However, these expansions were only approved because there was a demonstrated immediate public need. One expansion permit was appealed to the State Water Board, which clearly indicated that the Water Board should disapprove future such expansions into wetlands, and that local governments must complete the necessary planning to avoid this problem. Given the State Water Board’s position and the wetland provisions contained elsewhere in this Basin Plan, the Water Board will not approve further expansions of Bayfront landfills into wetlands. DEPARTMENT OF DEFENSE AND DEPARTMENT OF ENERGY PROGRAM

The goal of the DoD/DoE program is the investigation and cleanup of pollution at federal military sites. DoD sites include active and inactive military bases and formerly utilized defense (FUDs) sites. DoE sites include active federal energy agency sites. DoD and DoE sites in the Region as of 2005 are shown on Figure 4-7. An adjunct to cleanup, particularly with respect to DoD sites, is the return of these sites to productive, civilian use.

Investigation and cleanup at these sites follows the CERCLA process. For DoD sites, the DoD has elected to follow the CERCLA process even if the sites are not listed as “Superfund” sites. This process follows a rigorous sequence of document preparation and agency approvals including completion of the formal Preliminary Assessment, Site Investigation, Remedial Investigation, and Feasibility Study, all leading to a Record of Decision (ROD) on an acceptable Remedial Action Plan (RAP).

Groundwater cleanup must also adhere to the requirements of the Basin Plan and existing state law (the Water Code), relevant regulations (e.g., Title 27; Title 23, Chapter 16, etc.), and policies set forth by State Water Board Resolution Nos. 68-16, 88-63, and 92-49.

Under the Base Realignment and Closure Act of 1990 (amended 2005), the DoD has been conducting environmental investigation and cleanup at each of these sites with oversight from the Water Board and other agencies. There is considerable state and federal interest in moving these latter types of DoD sites into economically productive uses, in part to offset the negative economic impact of base closures on the local community or to invigorate the often depressed economies of local communities located near these sites. Progress has been slow in many cases due to competition for limited DoD cleanup funds, the complexities of the sites themselves, and uncertainty about the planned reuse. Cities have recently been pursuing “early transfers” that allow them to receive the military property prior to completion of cleanup. Local governments have contracted with developers and environmental firms to perform an integrated cleanup and redevelopment.

Closed military bases that are transferred to a local entity before the cleanup is complete may be subject to a land use covenant (LUC) issued by the Water Board to ensure the site cleanup is completed. The Water Board may issue SCRs per Water Code Section 13304 to allow investigation and cleanup after the military property is transferred. For additional regulatory tools, see Section 4.25.2 Requirements for Site Investigation, Cleanup, and Site Closure.

For the DoE program, all of the sites currently within the Region are active and are not expected to fall within public hands for the foreseeable future. Cleanup is ongoing at these sites. Contamination generally consists of discharges of solvents, petroleum hydrocarbons, PCBs, and/or metals to both soil and groundwater. In some cases, radionuclides have also been released. DoE has regulatory authority over radionuclide discharges, although the Water Board provides input into the investigation and cleanup activities related to them.

Federal funding for both the DoD and DoE programs covers all costs associated with Water Board and State Water Board staff oversight. The state signed a Cooperative Agreement with the Department of Defense (Defense-State Memorandum of Agreement, DSMOA)). In the Cooperative Agreement, DTSC acts as the state’s agent. Both the State Water Board and the Regional Water Boards coordinate with DTSC to allocate agency responsibility and funding and establish procedures under which site investigation and cleanup will proceed, decisions will be made, and disputes will be resolved. For the DoE program, a grant has been established which describes and funds Water Board oversight at DoE sites. ABOVEGROUND PETROLEUM STORAGE ACT

The state's Aboveground Petroleum Storage Act was enacted in 1989 and amended in 1991. The Act became effective on January 1, 1990.

The purpose of this Act is to protect the public and the environment from the serious threat of spillage of millions of gallons of petroleum-derived chemicals stored in thousands of aboveground storage tanks. The Act requires that the Water Board inspect aboveground petroleum storage tanks used for crude oil and its fractions for their compliance with the federally required Spill Prevention, Control, and Countermeasure Plan (SPCCP). In the event that a release occurs that threatens surface or groundwater, the Act allows the state to recover reasonable costs incurred in the oversight and regulation of the cleanup. The Water Board oversees sites where releases from aboveground storage tanks have impacted groundwater under the SLIC cost recovery program.


The intimate ties among the land, surface water, groundwater, the Estuary, and human activity must be acknowledged in order to promote wise, balanced, and sustainable use of water resources. In this regard, the Water Board will encourage planning and management by supplying tools and information that will provide an integrated environmental management approach to problem solving. It also must be recognized that groundwater quality and quantity are inextricably linked. Because an informed and involved citizenry is crucial to realizing groundwater protection, policies and plans should encourage and promote research, education, and public involvement as an integral part of any protection program. GROUNDWATER PROTECTION AND BENEFICIAL USE STUDIES

Water Board staff, with contributions from local agencies, evaluated existing groundwater protection programs and beneficial uses of groundwater in the Napa River Watershed (1996), San Francisco and Northern San Mateo Counties (1996), East Bay Plain, Alameda and Contra Costa Counties (1999), and South San Francisco Bay Basin, Alameda, San Mateo, and Santa Clara Counties (2003). Extensive research was conducted and numerous references were compiled to prepare these groundwater studies. In general, each study included the following goals:

  • Describe the hydrogeology and groundwater use for the groundwater basins;
  • Identify major threats to groundwater and groundwater protection programs;
  • Identify locations where groundwater is vulnerable to contamination;
  • Identify locations where groundwater monitoring is needed;
  • Use GIS to compile complex data sets to use as a decision-making tool for groundwater protection;
  • Refine beneficial use designations for some groundwater basins;
  • Identify inactive well locations;
  • Describe groundwater extraction for municipal, agricultural, and industrial water supply;
  • Summarize statewide initiatives for groundwater protection and data sharing; and
  • Evaluate special problem areas that are typically not addressed by groundwater protection programs.

The results of these groundwater protection studies identified several key groundwater protection issues that are summarized in Section 4.26 Emerging Program Areas. The reports are available at the Water Board website. STATE WATER BOARD GROUNDWATER PROTECTION PLANNING CONTRACT

At the Water Board's request, the State Water Board funded a contract with the University of California at Berkeley to develop a regional groundwater protection plan. The project focused on several significant groundwater basins: Santa Clara Valley, Niles Cone, Livermore Valley, San Mateo Plain, and Half Moon Bay Terrace (Table 2-2). The vulnerability to pollution of each of the basins was determined using the U.S. EPA's DRASTIC Index Method (U.S. EPA Project No. 600/2-87-035, April 1987) on a GIS. The project was completed in 1994 by the Center for Environmental Design Research, University of California at Berkeley. INTEGRATED ENVIRONMENTAL MANAGEMENT PROJECT

In 1987, the U.S. EPA completed the Integrated Environmental Management Plan (IEMP). This innovative study conducted in Santa Clara County sought to improve public health and environmental protection by integrating approaches for hazardous material management for land, air, and water. The IEMP's Drinking Water Subcommittee developed recommendations to address the question “How clean is clean?” The committee wrote, ".... because contamination and clean-up impacts vary significantly in different sites and different hydrogeologic zones, the Water Board should continue to develop and standardize a process for clean-up decision making, rather than establish across-the-board clean-up levels." The recommendations from this study were applied to developing site-specific cleanup levels. GROUNDWATER RESOURCE STUDY

A basin-wide approach for implementing and prioritizing groundwater cleanup was recommended in a series of reports titled "San Francisco Bay Region Groundwater Resource Study" (1987). The reports were a cooperative effort by the Water Board and the University of California at Berkeley, School of Public Health, and Department of Landscape Architecture. The ten volume series covered eight high priority groundwater basins: Niles Cone, Livermore and Sunol Valley, Ygnacio/Pittsburg/Clayton/San Ramon Basins, Suisun/Fairfield Basin, Napa Valley, Sonoma Valley, and San Mateo Basin. The Water Board used the results of this study to prioritize its workload in addressing polluted sites. SHALLOW DRAINAGE WELLS

The California Water Code, Section 13710, defines the term "well" or "water well" to mean any artificial excavation constructed by any method for the purpose of extracting water from, or injecting water into, the underground. The definition does not include (a) oil, gas, and geothermal wells, or (b) construction dewatering wells and hillside stabilization dewatering wells. Therefore, all shallow drainage wells (also known as dry wells, infiltration basins, and shallow injection wells) used for the purpose of disposing of stormwater or surface runoff are covered under this definition. The purpose of this Basin Plan section is to clarify the Water Board's position in regard to the construction, usage, and regulatory permitting aspects of shallow drainage wells.

In 1951, the Water Board adopted Resolution No. 81, "Statement of Policy on Sewer and Drainage Wells", which is incorporated by reference into this plan. This resolution states that the Water Board disapproves of the construction and use of wells for disposal of effluent from septic tanks and surface runoff from streets and highways except where such wells discharge into a formation that at no time will contain groundwater fit for domestic, agricultural, or industrial use. At the same time, the Water Board recognized that these wells already existed in the Region and that immediate abandonment may be impractical. Therefore no new installations were to be permitted, more satisfactory drainage methods were to be substituted for existing installations at the earliest practicable date, and the Water Board was to consider the matter of prescribing requirements for the discharge in granting any exceptions to the prohibition. After review of Water Board files, it does not appear as if any exceptions to the resolution were officially granted.

The Federal Underground Injection Control Program was established in 1984 with the adoption of the Safe Drinking Water Act. In California, the U. S. EPA is the lead agency in charge of administering the program. Under this program, wells used to dispose of surface water runoff are classified as Class V injection wells. The owner or operator of any existing Class V well is required to submit information on each well, including the nature and type of discharge and operating status. U.S. EPA is conducting a well inventory statewide to identify Class V wells.

There are a number of applicable state regulations pertaining to the construction and use of shallow drainage wells. AB2182 (Chapter 1131, Section 4458) of the California Health and Safety Code, passed in 1961, prohibits the use of drainage wells for the disposal of sewer water unless authorized by the Water Board. The Water Code (Chapter 10, Sections 13700 – 13806) defines the terms "well" and "water well" and states that any person who intends to dig, bore, or drill such a well must file a notice of intent with DWR or the designated local enforcement agency. A detailed report of completion must then be filed after construction. If the Water Board finds that standards of water well construction, maintenance, abandonment, and destruction are needed in any area to protect beneficial uses of groundwater, it shall determine the area to be involved and so report to each affected county and city in the area. Each such affected county shall, within 120 days of receipt of the report, adopt an ordinance establishing standards of water well construction, maintenance, abandonment, and destruction for the designated area. To date, standards and siting criteria for shallow drainage wells are non-existent in the Region and subsequently not included in the well-permitting process.

The Water Board issues NPDES permits for stormwater discharges to surface water for certain industrial and construction activities and to the larger municipalities in the Region (Section 4.14 Urban Runoff Management). The permits require the implementation of control measures to reduce pollutant loading, along with water quality monitoring to assure that the waters being discharged will not impact the beneficial uses of receiving waters. The discharge of industrial waste into the sanitary sewer system is now closely regulated under a pretreatment program. Likewise, the discharge of stormwater to the subsurface must also be regulated to assure the protection of groundwater supplies. Standards for shallow drainage well construction, maintenance, abandonment, destruction and siting criteria are needed throughout the Region. Land-use decisions, such as stormwater structural controls and well construction permitting, are most often made by local government agencies, including water districts, planning, and building departments. Many of these agencies are not aware of the Water Board's Resolution No. 81, or the rationale behind it.


The goal of the Shallow Drainage Program is to eliminate the unregulated construction and use of shallow drainage wells in areas where municipal, domestic, agricultural, and industrial groundwater supplies are threatened.

This goal is to be attained by a coordinated effort on the part of U.S. EPA, the Water Board, DWR, and local government agencies to implement a shallow drainage well control program.


The Water Board prohibits the unauthorized construction and use of shallow drainage wells. The shallow drainage well control program shall consist of two main elements: 1) locating existing wells; and 2) regulating the construction and use of existing and new wells.

1.Locating existing wells
U.S. EPA, the Water Board, and local government agencies will need to work together to identify all existing shallow drainage wells.
2.Regulating existing wells and new wells
Continued use of existing wells or construction of new wells may be authorized by a local enforcing agency through its well-permitting process. The Water Board will work with DWR and each city, county, and local water supply and flood control agency on developing standards for adoption by ordinance for the construction, maintenance, abandonment, and destruction of shallow drainage wells. Additionally, it must be demonstrated that the use of the well will not result in a discharge that may pose a threat to municipal, domestic, agricultural, and industrial groundwater supplies. If this cannot be adequately demonstrated, the well must be permanently closed. Closure of each well must be done in compliance with U.S. EPA Class V injection well closure guidelines and applicable local agency guidelines or regulations.


There are several aspects of protecting beneficial uses associated with aquatic systems and groundwater protection that have emerged as critical issues in recent years. This section presents a prospective view of emerging program areas that have increasingly become the focus of Water Board activity. Each involves both an integration of approaches used in current Water Board programs as well as innovative solutions.


As documented in the Habitat Goals reports, a large percentage of historic tidal marsh and mudflats around the Estuary have been diked, drained, and/or filled to serve various human purposes. Current planning efforts by multiple agencies recognize the importance of restoring wetland functions to the Estuary to protect and enhance beneficial uses. The Estuary Project’s Comprehensive Conservation and Management Plan (June 1994) proposes several goals for wetland management in the Estuary, and recommends large-scale restoration of salt ponds and other former wetlands in order to support sustainable populations of fish and wildlife as well as other benefits associated with wetlands. The Habitat Goals reports provide guidance to the Water Board and indicates where wetland restoration potential exists around the Estuary.

The Water Board participates in a number of wetland restoration projects in the Region, both in a regulatory role regarding proposed wetland fill and/or discharges, and in the role of an interested party or stakeholder, recognizing the multiple benefits of wetland restoration for water quality and beneficial uses. Major restoration projects underway include former salt ponds adjacent to South San Francisco Bay and San Pablo Bay, former DoD sites such as Hamilton Field in Marin County, and the Bair Island Ecological Reserve in South San Francisco Bay. While these projects are expected to have a positive impact on water quality and beneficial uses, certain challenges must be addressed, such as minimizing uptake of mercury into the food web, meeting water quality objectives for salinity and dissolved oxygen in discharges from ponds (impounded bay waters), protecting existing tidal mudflats, and controlling harmful invasive species such as Spartina alterniflora cordgrass and its hybrids.


San Francisco Bay has only recently been identified as a potential drinking water source, and this has become an emerging program area for the Water Board. Producing drinking water from saltwater results in a concentrated brine stream that must be managed to protect water quality. In the late 1990s, some water supply agencies in the Region began investigating the feasibility of producing drinking water from the Estuary using desalination technology. As of 2005, several sites are being screened for potential desalination facilities by various agencies, and in 2005 the Water Board issued an NPDES permit to one pilot plant for the Marin Municipal Water District in the City of San Rafael.

Desalination plants are in operation throughout the world, with facilities most common in the Middle East, the Caribbean and Florida. To date, only a limited number of desalination plants have been built along the California coast, primarily because the cost of desalination is generally higher than the costs of other water supply alternatives available in California (e.g., water transfers and groundwater pumping). However, as drought conditions occur and concern over water availability increases, desalination projects are being proposed at numerous locations in the state.

Desalination plants produce liquid wastes that may contain all or some of the following constituents: high salt concentrations, chemicals used to clean plant equipment and used during pretreatment, and toxic metals (which are most likely to be present if the discharge water was in contact with metallic materials used in construction of the plant facilities). Potential alternatives for disposal of liquid waste include discharge into waters of the state, combination with other discharges (e.g., power plant cooling water or sewage treatment plant effluent) before discharge, discharge into a sewer for treatment in a sewage treatment plant, or drying and disposal in a landfill. Desalination plants also produce a small amount of solid waste (e.g., spent pretreatment filters and solid particles that are filtered out in the pretreatment process).

If water supply agencies implement desalination to augment supplies along with waste management practices that protect beneficial uses, the Water Board will consider amending the Basin Plan to designate the municipal and domestic supply (MUN) beneficial use for applicable marine or estuarine areas of the Region.


As noted in Section Numeric Water Quality Objectives, Wasteload Allocations, there are pollutants of local concern for which water quality objectives have not been developed and adopted. Both regulatory and research surveillance programs periodically detect pollutants that are persisting in the aquatic environment, which may or may not have published guidelines for protecting beneficial uses. Such pollutants may be inducing toxicity or exhibiting bioaccumulation in the food web. The Regional Monitoring Program for the San Francisco Bay, described in Section 6.1 Regional Monitoring Program, includes studies to anticipate potential water quality problems by identifying previously unmonitored and/or unknown pollutants. It is through such efforts that the potential pollutant problems of the future can be identified and addressed before they become environmentally and economically costly “legacy” pollutants, such as mercury, PCBs, and chlorinated pesticides such as dichloro-diphenyl-trichloroethane (DDT). Absent regulatory objectives or published guidelines, the Water Board will encourage source identification and control of pollutants found in the Region’s waters that exhibit characteristics of concern, such as detectable and/or increasing levels in tissues of the Estuary’s organisms, as in the case of polybrominated diphenyl ethers (PBDEs). The Water Board will establish water quality objectives for selected pollutants as the necessary technical information becomes available.

Groundwater quality has been impacted by several emerging contaminants and by previously known contaminants that have undergone increased regulatory concern. Emerging contaminants, including N-nitrosodimethylamine (NDMA), disinfection byproducts such as trihalomethanes, haloacetic acids, bromate, and chlorite, endocrine disruptors, and pharmaceutically active compounds, may be present in sanitary wastewater, recycled water, imported water, and any other water source that receives sanitary wastewater. Emerging contaminants may pose a threat to groundwater quality when such waters are used for artificial recharge or are otherwise intentionally infiltrated. Other contaminants of concern affecting groundwater quality that are of concern include nitrate, total dissolved solids, perchlorate, solvent stabilizers (such as 1,4-dioxane), arsenic, and hexavalent chromium.


Groundwater protection studies conducted by Water Board staff identified several key groundwater protection issues and are summarized below. VERTICAL CONDUITS

Vertical conduits can provide pathways for the migration of surface pollution or shallow groundwater pollution into deeper water bearing zones. Pollutants that enter groundwater through vertical conduits circumvent the natural migration process, which protects groundwater by filtering and other natural attenuation processes. Numerous agricultural and domestic wells installed in the Region have been abandoned or covered by subsequent development. Identification and proper destruction of these potential conduits is critical to include in any groundwater protection program. HORIZONTAL CONDUITS/SANITARY SEWER LEAKS TO GROUNDWATER

Horizontal conduits also serve to spread contamination by providing preferential pathways for migration of contaminants and contaminated groundwater. Storm drain systems and their construction backfill can be significant pathways for migration of contaminated shallow groundwater to water bodies where the storm drains discharge. Similar protocols should be followed for investigating horizontal conduits as for vertical conduits. A horizontal conduit study should be conducted at all sites where releases of toxic or hazardous materials are documented and before development or new construction begins at sites where toxic or hazardous materials have been used or stored. This is particularly important at or near dry cleaners or other operations where chlorinated solvents have been used.

Sanitary sewer lines may also allow pollutants to migrate to groundwater. Exfiltration is leakage from sanitary sewer lines into the subsurface and, in most cases, into surrounding groundwater. This phenomenon usually occurs in areas where the water table is below the sewer line. Leaking sewer lines can introduce pathogens into surrounding groundwater. Of more significance are chemicals transported in sewer lines that are released and migrate to and affect both shallow and deeper aquifers. The most significant historical impacts of leaking sewer lines are often associated with dry cleaning operations and the use of chlorinated solvents in electronics industries, such as wafer fabricators, plating shops, and printed circuit board shops. GROUNDWATER SURFACE WATER INTERACTIONS

Nearly all surface water features (streams, lakes, reservoirs, wetlands, and estuaries) interact with groundwater. Several issues have been identified that simultaneously affect the quality and quantity of surface water and groundwater due to the dynamic relationship between the two. The effects of these issues on water quality and quantity must be understood in order to develop effective water resource management strategies. These issues include the effect of surface water diversion and groundwater withdrawal on creek and riparian habitat, water quality, surface water infiltration to groundwater (e.g., recharge and stormwater infiltration), groundwater discharge to surface water (e.g., plume discharges), and changing land use (as it affects runoff and recharge). SALTWATER INTRUSION

Saltwater from San Francisco Bay and adjacent salt ponds has intruded freshwater-bearing aquifers in the Niles Cone, Santa Clara Valley, and San Mateo Plain basins. In both the Niles Cone and Santa Clara Valley basins, local agencies have implemented measures to prevent saltwater intrusion. The threat of saltwater intrusion in the Niles Cone is primarily due to the basin’s proximity to San Francisco Bay and the large system of salt ponds that operate along the Bay’s margin. In Santa Clara County, land subsidence, resulting from historical pumping that lowered the water table, has caused the lower reaches of streams and rivers to be invaded by saline tidal waters, increasing salinity in shallow groundwater. Land subsidence is no long occurring in Santa Clara Valley. TRACKING INSTITUTIONAL CONTROLS

Due to the difficulty of accomplishing rapid cleanup at most sites, it is usually necessary to manage site contamination to avoid or minimize exposure pending attainment of cleanup standards. Risk management measures include engineering controls (such as slurry walls or engineered caps) and institutional controls (such as notifications to site occupants or deed restrictions prohibiting sensitive land uses). Because risk management measures usually need to remain effective for many years, their effective implementation needs to be tracked and enforced. At issue is how best to do this. The solution will involve some combination of oversight by the Water Board or other cleanup oversight agency, the local permitting agency, and the discharger.


Sediments in the larger Estuary are both sources and sinks of pollutants. Under the Bay Protection and Toxic Cleanup Program in 1999, The Water Board completed a detailed assessment of (a) the levels of pollutants in sediment throughout the Bay, and (b) the risks and benefits of cleaning or otherwise managing existing hot spots.

Pollutant transport associated with sediments is also the subject of numerous studies, many of which are supported by the Water Board. The dynamics of sediment movement, uptake of pollutants through the benthic food web, measurement of pollutant levels on suspended material, and food web models associated with TMDL projects are examples of such studies.

Finally, the environmental effects associated with the disposal or reuse of Estuary sediments have been extensively investigated within the context of the Water Board's dredging management program. As part of this effort, the Water Board has supported detailed research on developing sediment toxicity tests and sediment quality objectives.


The U.S. EPA, National Oceanic and Atmospheric Administration (NOAA), and a number of other federal agencies announced the “Portfields” initiative in 2003. This effort is a renewed focus on revitalizing the nation’s port communities to protect the coastal environment and restore or maintain economic vitality. Many waterfront areas have suffered as waterfront-manufacturing industries changed their interests or went abroad. Abandoned properties with perceived contamination can prevent redevelopment, and local communities lose jobs and other economic benefit. Businesses that are today seeking viable waterfront lands for manufacturing, shipping, and tourism can benefit from Portfields revitalization projects. There are significant waterfront industrial areas in the Region that have undergone redevelopment, such as the Port of Oakland and Mission Bay, and more are expected as federal agencies direct funding to Brownfield project proponents in port areas.


Hydromodification is a general term that encompasses effects of projects on the natural hydrologic, geochemical and physical functions of streams and wetlands that maintain or enhance water quality. Regional Water Boards use this term to describe an alteration away from a natural state of stream flows or the beds or banks of rivers, streams, or creeks, including ephemeral streams, which results in hydrogeomorphic changes. Protecting beneficial uses within the Region consistent with the federal Clean Water Act and the Porter-Cologne Act requires careful consideration of projects that result in hydrogeomorphic changes and related adverse impacts to the water quality and beneficial uses of waters of the State.

An increasing number of Water Board regulatory actions pertain to the proposed hydromodification of stream and river systems in the Region. These actions include water quality certifications or waste discharge requirements for projects that apply for Clean Water Act Section 401 Certification, total maximum daily loads (TMDLs) for sediments and nutrients in some of the Region’s streams, and requirements for municipal stormwater management programs to develop Hydromodification Management Plans. Additionally, many of the grants for clean water awarded under voter-approved bond measures and managed by Water Board staff involve restoration proposals on various components of stream systems. To ensure protection of streams through its regulatory and grant programs, and increase efficiency of the application process, Water Board staff developed a technical reference circular (Circular) in 2003, entitled, “A Primer on Stream and River Protection for the Regulator and Program Manager.” The purpose of the Circular is to help various agency staff and permit applicants recognize the linkages between water quality and the good physical conditions of stream channels. The Water Board will consider amending the water quality standards and implementation program to clarify the dependence of water quality and beneficial uses on the functions and physical characteristics of water bodies.


Figure 4-1: Publicly Owned Treatment Works (POTWs)

Figure 4-2: Industrial Dischargers

Figure 4-3: Urban Areas in San Francisco Bay Basin

Figure 4-4: Dredged Material Disposal Sites

Figure 4-5: Inactive Mine Sites

Figure 4-6: Municipal Solid Waste Landfill Sites in the Region

Figure 4-7: Department of Defense and Department of Energy Sites


Table 4-1: Discharge Prohibitions

Table 4-2: Effluent Limitations for Conventional Pollutants

Table 4-3: Acute Toxicity Effluent Limits

Table 4-4: Critical Life Stage Toxicity Test Species and Protocols

Table 4-5: Conditions that Require Monthly Monitoring of Toxicity Levels

Table 4-6: Dilution Credits for Calculation of Cyanide Water Quality-based Effluent Limits for Shallow Water Dischargers

Table 4-8: Publicly Owned Treatment Works (POTWs)

Table 4-9: Major Industrial Discharge Outfalls

Table 4-10: Status of Urban Runoff Control Programs

Table 4-11: Goals of Long Term Management Strategy

Table 4-12: Potential Consequences and Impacts of Dredging and Dredged Material Disposal

Table 4-13: Long Term Management Strategy Participants

Table 4-14: Dredged Material Volume Targets

Table 4-15: Transition Volume Targets for In-Bay Disposal of Dredged Materials

Table 4-16: Inactive Mine Sites

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