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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.

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