7.3 Water Quality Attainment Strategies and TMDLs for the Marin Coastal Basin (see Figure 2-3)

7.3.1 Tomales Bay Watershed Pathogens TMDL

The overall goal of the Tomales Bay Watershed Pathogens Total Maximum Daily Load (TMDL) is to ensure protection of water contact recreational uses and Bay shellfish harvesting, thereby minimizing human exposure to disease-causing pathogens. The following sections establish a density-based pathogens TMDL for Tomales Bay and its tributaries, and actions and monitoring necessary to implement theTMDL. The TMDL defines allowable density-based water quality bacteria concentrations and prohibits the discharge of human waste. The associated implementation plan specifies the actions necessary to protect and restore beneficial uses. This TMDL strives to achieve a balance that allows human activities including agriculture, recreation, commercial fishing and aquaculture, and residential use to coexist and also restores and protects water quality. As outlined in the adaptive implementation section, the effectiveness of implementation actions, monitoring to track progress toward targets, and the scientific understanding pertaining to pathogens will be periodically reviewed and the TMDL may be adapted as warranted.

In addition to pathogens, animal and human waste contain nutrients that pose a threat to aquatic ecosystem beneficial uses. Tomales Bay, Walker Creek, and Lagunitas Creek are listed as impaired by excess nutrients. Human and animal wastes may also contain other harmful constituents such as steroids and pharmaceuticals. In addition to protecting pathogen-impaired beneficial uses such as shellfish harvesting, water contact recreation, and non-contact water recreation, by eliminating the discharge of human waste and controlling the discharge of animal waste, this TMDL will also protect aquatic ecosystem beneficial uses such as marine habitat, estuarine habitat, cold and warm freshwater habitat, and wildlife habitat from other harmful constituents found in human and animal waste.

7.3.1.1    Problem Statement

Monitoring results for Tomales Bay and its main tributaries (Lagunitas, Walker, and Olema creeks) indicate that these waters exceed bacteria water quality objectives for shellfish harvesting and recreational waters (Table 3-1) and, as such, are impaired by pathogens. The presence of pathogens is inferred from high concentrations of fecal coliform bacteria (a commonly used indicator of human pathogenic organisms). Pathogen pollution is adversely affecting existing beneficial uses, which include shellfish harvesting (i.e., sport and commercial oyster, clam, and mussel harvesting), water contact recreation (i.e., swimming, fishing) and non-contact water recreation (i.e., boating, kayaking).

This TMDL addresses the following pathogen-impaired water bodies in the Tomales Bay Watershed:

• Tomales Bay
• Lagunitas Creek
• Walker Creek
• Olema Creek

7.3.1.2    Sources

If not properly managed, the following Tomales Bay Watershed sources have the potential to discharge pathogens to surface waters: on-site sewage disposal systems (OSDSs), small wastewater treatment facilities and sewage holding ponds, boat discharges, grazing lands, dairies, equestrian facilities, and municipal runoff. Pathogens sources are identified based on elevated coliform bacteria levels downstream of identified land uses or facilities and from documentation of inadequately treated human waste discharges.

• The Walker Creek watershed is dominated by grazing lands. Coliform bacteria levels and coliform loads from the Walker Creek watershed are extremely high during storm periods and a significant coliform source to Tomales Bay.
  
• High coliform levels detected in storm drains indicate that municipal runoff is a pathogens source.
  
• High coliform levels and loads downstream of residential homes and equestrian facilities suggest that failing septic systems, municipal runoff, and equestrian facilities are coliform sources.
  
• The Water Board regulates ten small wastewater treatment facilities and sewage holding ponds and prohibits direct discharges from these facilities into Tomales Bay or its tributaries. Four facilities have holding ponds and are permitted to discharge treated effluent to irrigation fields in the dry season. The other six wastewater treatment facilities utilize leach fields for dispersing treated effluent. Accidental malfunctions, including the breaching of ponds, a break in a sewage line, or land application when soil is saturated or it is raining, could result in discharge of untreated or partially treated effluent. Therefore, these facilities are considered potential sources.
  

In addition to the above sources, warm-blooded mammals and birds that reside in the watershed and Bay produce coliform bacteria. During non-storm periods Tomales Bay coliform levels are typically below the water quality objectives for shellfish harvesting waters, indicating that in-Bay wildlife such as seals and birds are not significant sources. Approximately 30% of the lands draining to Tomales Bay are open space forested lands. Water quality monitoring of a watershed on the western shoreline of Tomales Bay with minimal human influences suggests that waters draining open space areas are below tributary bacteria water quality objectives and therefore terrestrial wildlife are nota significant source.

7.3.1.3    Numeric Targets

Table 7.3.1-1 contains the numeric water quality targets for the Tomales Bay Watershed Pathogens TMDL. The coliform bacteria targets are based on fecal coliform bacteria concentrations aimed at protecting shellfish harvesting and contact and non-contact water recreation beneficial uses. These density-based numeric targets define bacterial densities associated with minimal risk to humans and are the same as the water quality objectives contained in Table 3-1. The Tomales Bay targets are intended to protect the most sensitive beneficial use, shellfish harvesting. The tributary targets are intended to protect recreational uses. An additional numeric target for Tomales Bay is expressed as the number of days commercial shellfish growing areas are subjected to harvest closures due to elevated water column bacteria densities. Consistent with the definition of “threatened conditions” in the California Shellfish Protection Act, Tomales Bay shellfish growing areas shall not be closed for harvest for more than 30 days per calendar year. The California Department of Health Services requires shellfish growing areas to close for harvesting when 24-hour and 10-day rainfall totals exceed established thresholds. Rainfall thresholds are established based on the relationship between rainfall and observed fecal coliformlevels in Bay waters and shellfish.

In addition, no human waste (raw sewage or inadequately treated waste) shall be discharged to Tomales Bay or its tributaries. The no human waste discharge target is consistent with Discharge Prohibitions 5 and 15, contained in Table 4-1. This target is necessary because human waste is a significant source of pathogenic organisms, including viruses; and attainment of fecal coliform targets alone may not sufficiently protect human health. The coliform bacteria targets, in combination with the human waste discharge prohibitions and the shellfish harvesting closure targets, are the basis for the TMDL and load allocations, and fully protect beneficial uses.

7.3.1.4    Total Maximum Daily Load

Table 7.3.1-2 lists the Tomales Bay Watershed Pathogens TMDL. The TMDL consists of the density-based coliform bacteria TMDL targets. The TMDL ensures protection of water contact recreational uses and Bay shellfish harvesting, thereby minimizing human exposure to disease causing pathogens.

7.3.1.5    Load Allocations

TMDL targets are an interpretation of water quality standards, whereas TMDL allocations specify the amount (or concentration) of a pollutant that can be discharged to a waterbody such that standards are attained in both the receiving waterbody and all downstream waters. Table 7.3.1-3 presents density-based load allocations for Tomales Bay watersheds pathogens source categories that implement tributary targets, and Table 7.3.1-4 presents allocations to major tributaries, where they discharge to Tomales Bay, and implement the Bay targets. Load allocations to the tributaries reflect the highest fecal coliform concentrations that can be discharged while still attaining and maintaining the Bay shellfish harvesting water quality objectives. All entities in a watershed are responsible for meeting their source category allocation (Table 7.3.1-3) and the applicable geographic-based allocations (Table 7.3.1-4).

Discharging entities will not be held responsible for uncontrollable coliform discharges originating from wildlife. If wildlife contributions are determined to be the cause of exceedances, the TMDL targets and allocation scheme will be revisited as part of the adaptive implementation program. The discharge of human waste is prohibited. All sources of human waste have an allocation of zero. Nonpoint source runoff containing coliform bacteria of animal and wildlife origin, at levels that do not result in exceedances of water objectives, does not constitute wastewater with particular characteristics of concern to beneficial uses. Therefore, animal- and wildlife-associated discharges, in compliance with the conditions of this TMDL, do not constitute a violation of applicable discharge prohibitions.

7.3.1.6    Implementation Plan

The Tomales Bay Watershed Pathogens TMDL Implementation Plan builds upon previous and ongoing successful efforts to reduce pathogen loads in Tomales Bay and its tributaries. The plan requires actions consistent with the California Water Code (CWC 13000 et seq.), the state’s Nonpoint Source Pollution Control Program Plan (CWC Section 13369), the Policy for Implementation and Enforcement of the Nonpoint Source Pollution Control Program (State Water Resources Control Board. 2004. Policy for Implementation and Enforcement of the Nonpoint Source Pollution Prevention Control Program), and human waste discharge prohibitions (Prohibitions 5 and 15, Table 4-1).

This plan specifies required implementation measures (Table 7.3.1-5) for each of the source categories (Table 7.3.1-3). These implementation measures include evaluation of operating practices, development of comprehensive site-specific pathogens control measures and an implementation schedule for such management measures, and submittal of progress reports documenting actions undertaken. Progress reports may be submitted directly to the Water Board or, if designated, through third parties. These progress reports will serve as documentation that source reduction measures are being implemented. While third parties may provide valuable assistance to TMDL implementation, the discharger is the entity responsible for complying with the specified regulations and regulatory controls. Responsible parties within each source category are required to implement the measures as specified in Table 7.3.1-5. The numeric targets and load allocations are not directly enforceable. For purpose of demonstrating attainment of applicable allocations, responsible parties will only be responsible for compliance with specified implementation measures and applicable waste discharge requirements or waiver conditions.

The state’s Policy for Implementation and Enforcement of the Nonpoint Source Pollution Control Program requires that current and proposed nonpoint source discharges are regulated under waste discharge requirements (WDRs), waiver of waste discharge requirements, Basin Plan prohibitions, or some combination of these tools. Table 7.3.1-5 describes the method that will be used to regulate dischargers in each source category. The Water Board has established conditions for waiving WDRs for dairies. The Water Board intends to work with stakeholders to develop similar waiver conditions for grazing lands and equestrian facilities by 2009.

Agricultural Water Quality Control Program Costs

The implementation measures for grazing lands and dairies constitute an agricultural water quality control program and therefore, consistent with California Water Code requirements (Section 13141), the cost of the program is estimated herein. The total program implementation cost for these agricultural sources is estimated to range between $900,000 – $2 million per year over the next 10 years. The estimated cost will be shared by Tomales Bay watershed grazing lands operators (approximately 150). This estimate includes the cost of implementing animal waste control and grazing management measures and is based on costs associated with technical assistance and evaluation, installation of water troughs, and cattle control fencing along all streams. The program cost estimate may be high as it does not account for implementation actions already underway or areas that may not require fencing. Besides fencing, other acceptable methods of managing livestock access to streams are not included in this cost estimate due to variability in costs and site specific applicability. Potential financing sources include federal and state water quality grants and federal agricultural grants.

Evaluation and Monitoring

Dischargers, stakeholders, and Water Board staff will conduct water quality monitoring to evaluate fecal coliform concentration trends in Tomales Bay and its tributaries. Five years after TMDL adoption, the Water Board will evaluate monitoring results and assess progress made toward attaining TMDL targets (Table 7.3.1-1) and load allocations (Table 7.3.1-3 and Table 7.3.1-4).

In 2009 and approximately every five years after the adoption of the TMDL, the Water Board will evaluate site specific, sub-watershed specific, and watershed-wide compliance with the trackable implementation measures specified in Table 7.3.1-5. In evaluating compliance with the trackable implementation measures, the Water Board will consider the level of participation of each source category as well as individual dischargers (as documented by Water Board staff or third parties).

If a discharger demonstrates that all implementation measures have been undertaken or that it is infeasible to meet their allocation due to wildlife contributions, the Water Board will consider revising allocations as appropriate. If source control actions are fully implemented throughout the Watershed and the TMDL targets are not met, the Water Board may consider re-evaluating or revising the TMDL and allocations. If, on the other hand, the required actions are not fully implemented, or are partially implemented, the Water Board may consider regulatory or enforcement action against parties or individual dischargers not in compliance.

The California Department of Health Services, working in consultation with the Shellfish Technical Advisory Committee, is encouraged to periodically evaluate, beginning in 2009, shellfish harvest closure guidelines and the relationship between precipitation, runoff, coliform levels, and water quality exceedances.

In order to assess water quality improvements and obtain additional information for further refinement of the TMDL, Water Board staff and stakeholders will collaborate in monitoring efforts. The main objectives of the Monitoring Program are to:

• Assess attainment of TMDL targets;
• Evaluate spatial and temporal water quality trends in the Bay and its tributaries;
• Further identify significant pathogens source areas;
• Evaluate coliform levels and loadings to the Bay at the terminus of major tributaries.
• Collect sufficient data to calibrate and validate the Bay hydrodynamic model to observed coliform levels; and
• Collect sufficient data to prioritize implementation efforts and assess the effectiveness of implementation actions.

Table 7.3.1-7 outlines the locations, constituents, sampling frequency, analytical methods, and the sampling entities for a baseline water quality monitoring program. Additional monitoring will be conducted as needed if funds are available. The Water Board, in coordination with the sampling entities and interested third parties, such as National Park Service, California Department of Health Services, commercial shellfish growers, the Inverness Public Utility District, and the Salmon Protection and Watershed Network will implement this long-term water quality monitoring program. All water quality monitoring (including Quality Assurance and Quality Control procedures) will be performed pursuant to the State Water Board’s Quality Assurance Management Plan for the Surface Water Ambient Monitoring Program.

Adaptive Implementation

Approximately every five years, the Water Board will review the Tomales Bay Watershed Pathogens TMDL and evaluate new and relevant information from monitoring, special studies, and scientific literature. The reviews will be coordinated through the Water Board’s continuing planning program and will provide opportunities for stakeholder participation. Any necessary modifications to the targets, allocations, or implementation plan will be incorporated into the Basin Plan. In evaluating necessary modifications, the Water Board will favor actions that reduce sediment and nutrient loads, pollutants for which the Tomales Bay Watershed is also impaired. At a minimum, the following questions will be used to conduct the reviews. Additional questions will be developed in collaboration with stakeholders during each review.

1. Are the Bay and the tributaries progressing toward TMDL targets as expected? If progress is unclear, how should monitoring efforts be modified to detect trends? If there has not been adequate progress, how might the implementation actions or allocations be modified?
   
2. What are the pollutant loads for the various source categories (including naturally occurring background pathogen contributions and the contribution from open space lands), how have these loads changed over time, how do they vary seasonally, and how might source control measures be modified to improve load reduction?
   
3. Is there new, reliable, and widely accepted scientific information that suggests modifications to targets, allocations, or implementation actions? If so, how should the TMDL be modified?
   
4. The allocations assume a conservative bacterial die-off rate of 0.02 per hour. This value is based on rates reported for San Francisco Bay in 1970. If bacterial die-off is found to be higher, higher allocations may be considered. What are bacterial die-off rates in the water column and stream sediments? Do they vary by season? What are bacteria transport times from sources to the Bay?
   
5. How does estuarine mixing and dilution of tributary waters vary by flow and season?
   
6. What is the relationship between precipitation, runoff, tributary loads, Bay coliform levels, and water quality exceedances and shellfish harvesting closures?
   
7. Are there bacteria in Tomales Bay sediments that enter the water column during storm events? If yes, how should this process be accounted for?

If it is demonstrated that all reasonable and feasible source control measures have been implemented for a sufficient period of time and TMDL targets are still not being met, the Water Board will reevaluate water quality standards, TMDL targets and allocations as appropriate.

7.3.2 Total Maximum Daily Load for Mercury in Walker Creek and Soulajule Reservoir

Walker Creek and Soulajule Reservoir, which is located in the Walker Creek watershed, are impaired by mercury. This TMDL applies to Soulajule Reservoir and the freshwater portions of Walker Creek. The goal of the TMDL is to establish and maintain environmental conditions that will support beneficial uses of these waters established in Chapter 2.

The following sections establish a concentration-based TMDL for mercury in the Walker Creek watershed, and prescribe actions and monitoring necessary to implement and maintain the TMDL. The numeric targets, allocations, and associated implementation plan will ensure that Walker Creek and Soulajule Reservoir attain applicable water quality standards and achieve the TMDL.

The TMDL allocations and implementation plan are designed to control the amount of mercury discharged to Walker Creek and from Soulajule Reservoir, and prescribe and promote actions to minimize the potential for mercury to be present in the toxic and bioavailable form, methylmercury. Effectiveness of implementation actions, monitoring to track progress toward targets, and the scientific understanding pertaining to mercury will be periodically reviewed. The TMDL may be adapted as warranted.

7.3.2.1    Problem Statement

Walker Creek and Soulajule Reservoir are impaired because mercury adversely affects beneficial uses, including wildlife habitat and all uses supporting aquatic life.

• Mercury concentrations in Walker Creek exceed the mercury freshwater aquatic life acute toxicity objective established to protect aquatic organisms (Table 3.4).
• Terrestrial species that primarily or exclusively eat fish (such as piscivorous birds, the most sensitive wildlife species in the watershed) are at risk from exposure to mercury due to its tendency to bioaccumulate in the food web. Because mercury concentrations in Walker Creek fish are high enough to threaten the health of piscivorous birds, the narrative bioaccumulation objective (see Chapter 3) and numeric aquatic organism and wildlife mercury water quality objective (Table 3-4a) are not being met.
  
• Soulajule Reservoir is impaired because some fish in the reservoir exceed mercury levels considered safe for human consumption.
  
• The beneficial use aimed at protecting the health of people who choose to consume Soulajule Reservoir fish (REC1) is impaired and the narrative bioaccumulation water quality objective is not being met.
  
• In 2004, the California Office of Environmental Health Hazard Assessment issued an interim advisory recommending that people limit consumption of reservoir fish due to elevated mercury levels. 

7.3.2.2    Sources

The following sources have the potential to discharge mercury to surface waters in the Walker Creek watershed:

• Gambonini Mine site – An inactive mercury mine and the largest mercury processing facility in the watershed. Mining waste was not properly contained on-site, and consequently the site discharged large quantities of mercury-laden sediments prior to cleanup (initiated in 1998).
  
• Soulajule Watershed and Reservoir – Two abandoned mercury mines are located in this watershed. Soulajule Reservoir discharges into Walker Creek just downstream of the Gambonini Mine drainage.
  
• Downstream depositional features – Mercury-laden sediments in depositional areas (creek beds, banks, and floodplains) downstream of the mercury mines, which discharge mercury to the creek during storms.
  
• Background – Mercury is present at low concentrations throughout the watershed. Background levels account for atmospheric deposition and naturally occurring mercury found in the watershed’s soils. The Walker Creek watershed background suspended sediment mercury concentration is 0.2 mg mercury per kg dry sediment.

7.3.2.3    TMDL Targets

• To protect wildlife and rare and endangered species, the mercury concentration in fish consumed by piscivorous birds shall not exceed 0.05 mg mercury per kg fish, measured in whole fish 5–15 cm in length, average wet weight nor shall it exceed 0.1 mg mercury per kg fish, measured in whole fish 15-35 cm in length, average wet weight. The goal of these targets, which are consistent with the bioaccumulation objective in Chapter 3, is to ensure that controllable water quality factors do not cause detrimental mercury concentrations in Walker Creek and Soulajule Reservoir wildlife.
  
• To protect aquatic organisms, water column mercury concentrations shall not exceed the water quality objective of 2.4 µg/l (one-hour average).
  
• To protect humans who consume Soulajule Reservoir and Walker Creek fish (assuming future conditions allow for the consumption of Walker Creek fish), water column mercury concentrations shall not exceed the California Toxics Rule (CTR) criterion of 0.050 µg/l (averaged over a 30-day period).

7.3.2.4    Allocations and Total Maximum Daily Load

The TMDL for Walker Creek is 0.5 mg mercury per kg suspended sediment and the TMDL for Soulajule Reservoir is 0.04 ng dissolved methylmercury per liter water. Concentration-based load allocations for Walker Creek and Soulajule Reservoir mercury sources are shown in Table 7.3.2-1.

7.3.2.5    Implementation Plan

The implementation plan builds upon previous and ongoing successful efforts to reduce mercury loads in Walker Creek and its tributaries. Table 7.3.2-2 contains the required implementation measures for each source.  It is important to note that the numeric targets and load allocations in the TMDL are not directly enforceable. To demonstrate attainment of applicable allocations, responsible parties must demonstrate compliance with specified implementation measures and any applicable waste discharge requirements (WDRs) or waiver conditions.

Cost Estimate: Agricultural Water Quality Control Program

Because the implementation measures for grazing lands constitute an agricultural water quality control plan, the cost of that program is estimated below, consistent with California Water Code requirements (Section 13141). We estimate that 100 percent of the downstream depositional areas can be considered grazing lands. Costs estimated for reducing mercury discharges and methylmercury production on grazing lands are $1.5 to 2.5 million over a ten-year period. These costs are associated with reducing sediment discharges and enhancing habitat conditions on Walker Creek and its tributaries. Considering potential benefits to the public in terms of habitat restoration and water quality, we expect that a significant portion of the costs will be paid for with public funds.

Evaluation and Monitoring

Water Board staff will conduct water quality monitoring to evaluate mercury concentrations in Walker Creek and its tributaries as part of the Surface Water Ambient Monitoring Program (SWAMP). Marin Municipal Water District will conduct water quality monitoring to evaluate mercury concentrations in both Soulajule Reservoir and reservoir discharges to Arroyo Sausal Creek. All water quality monitoring (including quality assurance and quality control procedures) will be performed pursuant to the State Water Board’s Quality Assurance Management Plan for this program. The main objectives of the monitoring are:

• Assess attainment of TMDL targets and load allocations
• Evaluate spatial and temporal water quality trends
• Refine understanding of mercury loading in downstream depositional areas
  
• Refine understanding of methylmercury production and bioaccumulation in Soulajule Reservoir
  
• Collect sufficient data to prioritize implementation efforts and assess the effectiveness of source control actions
  

Table 7.3.2-3 presents locations in the Walker Creek watershed for baseline water quality monitoring. These sites will be monitored for suspended particulate, methyl- and total mercury concentrations during the wet and dry seasons. Fish tissue mercury concentrations will be monitored to aid in understanding mercury and the food web. Mercury concentrations in fish of the size typically consumed by wildlife and humans will be monitored in Soulajule Reservoir to assess progress towards attaining the wildlife and human health target. Wet season sampling will focus on characterizing conditions during peak flow events. SWAMP monitoring will be conducted based on availability of funds.

Walker Creek Ranch is considered an “integration” site for the watershed. Water quality data collected at Walker Creek Ranch integrates Salmon Creek background concentrations with loads from the Gambonini Mine Site, Soulajule Reservoir, and some downstream depositional features. Mercury levels in 5–15 cm fish in Walker Creek will be monitored every five years at Walker Creek Ranch to assess progress towards attaining the wildlife target. In addition, the Water Board, in cooperation with the United States Geological Survey, maintains a continuous data recorder at Walker Creek Ranch that monitors suspended sediment and particulate mercury concentrations in Walker Creek.

Five years after adoption of this TMDL, the Water Board will evaluate monitoring results and assess progress made toward attaining targets and load allocations. Beginning in 2012 and approximately every five years thereafter, the Water Board will evaluate site specific, sub-watershed-specific, and watershed-wide compliance with the trackable implementation measures specified in Table 7.3.2-2.

Adaptive Implementation

Approximately every five years, the Water Board will review the Walker Creek Mercury TMDL and evaluate new and relevant information from monitoring, special studies, and the scientific literature. At a minimum, the following questions will be incorporated into the reviews. Additional questions will be developed in collaboration with stakeholders during each review cycle.

• Are Walker Creek and its tributaries progressing toward TMDL targets as expected? If progress is unclear, how should monitoring efforts be modified to detect trends? If there has not been adequate progress, how should the implementation actions or allocations be modified?
  
• What are the pollutant loads for the various sources? Have these loads changed over time? How do they vary seasonally? How might source control measures be modified to improve load reduction?
  
• What wetland and creek restoration methods should be used to minimize mercury discharges and methylmercury production while enhancing and restoring habitat values?
  
• Are wildlife feeding in Soulajule Reservoir at risk? If so, how can the Reservoir be managed to reduce this risk?
  
• Does additional sediment, water column, or fish tissue total or methylmercury data support our understanding of linkages in the watershed or suggest an alternative allocation strategy?
  
• Is there new, reliable, and widely accepted scientific information that suggests modifications to targets, allocations, or implementation actions? If so, how should the TMDL be modified?
  

Reviews will be coordinated through the Water Board’s continuing planning program, with stakeholder participation. Any necessary modifications to the targets, allocations, or implementation plan will be incorporated into the Basin Plan via an amendment process. In evaluating necessary modifications, the Water Board will favor actions that reduce sediment and nutrient loads, pollutants for which the Walker Creek is also impaired.

7.3.3  Lagunitas Creek Fine Sediment Reduction and Habitat Enhancement Plan

The following sections establish:

• A sediment TMDL defining the allowable amount of sediment that can be discharged into the Lagunitas Creek watershed, expressed as a percentage of the natural background sediment delivery rate to channels; and
• An implementation plan to achieve the TMDL and substantial habitat enhancement in channel reaches that support coho salmon, steelhead, and/or California freshwater shrimp.

The goals of the Lagunitas Creek Sediment Reduction and Habitat Enhancement Plan (Plan) are as follows:

• To restore an annual spawning run within the Lagunitas Creek watershed of 1300-or-more adult coho salmon, achieved for at least twelve consecutive years.
• For native fish and aquatic wildlife species to be in good condition at the individual, population, and community levels.
• To protect and enhance the aesthetic and recreational values of the creek and its tributaries.

The main focus of this Plan is habitat enhancement, because habitat loss and simplification appears to be a primary cause of the declines of watershed populations of coho salmon, steelhead, and California freshwater shrimp.  The Plan also establishes a regulatory program to reduce sediment delivery to channels resulting from road-related erosion, a necessary condition to support recovery of listed species and achieve water quality objectives for sediment and settleable material. Other significant land-use related sediment sources are already being reduced substantially through existing regulatory programs and/or natural recovery processes.

7.3.3.1         Problem Statement

Due to excess erosion and sedimentation in the Lagunitas Creek watershed, the narrative water quality objectives for sediment and settleable material are not being met, and cold freshwater habitat, wildlife habitat, fish spawning, recreation, and preservation of rare and endangered species beneficial uses are impaired.  In addition, the narrative water quality objective for population and community ecology is not being met due to habitat simplification, which is a primary cause for the decline of coho salmon and steelhead trout populations.

Lagunitas Creek provides essential habitat for coho salmon, steelhead trout, and California freshwater shrimp, all of which are listed under the federal Endangered Species Act (coho salmon and California freshwater shrimp also are listed under the California Endangered Species Act).  During the historical period - the mid-nineteenth century through present - there has been a precipitous decline in the abundance of coho salmon and steelhead in the Lagunitas Creek watershed.  Coho salmon and steelhead runs once numbered in the several thousands.  Up until the late 1960s, Lagunitas Creek was a popular destination for sport fisherman hoping to catch steelhead and coho salmon.  In 1996, Lagunitas Creek’s salmon and steelhead populations had dropped so low that they were listed under the Endangered Species Act. 

The most important causes for coho salmon and steelhead population declines in the Lagunitas Creek watershed appear to be: a) the loss of about half of the potential habitat, which has been inundated and/or is no longer accessible as a result of dam construction; and b) in almost all the remaining habitat, the fact that channel incision has greatly simplified habitat and disconnected the channel from its floodplain.

Channel incision causes habitat simplification, which herein is defined as the progressive lowering over time of the streambed elevation as a result of net erosion.  San Geronimo and Lagunitas creeks and alluvial reaches of their tributaries have incised substantially during the historical period. Channel incision obliterates the basic physical habitat structure of the channel, expressed by a substantial reduction in the frequency and area of gravel bars, riffles, and side channels. If a channel incises substantially, it will become disconnected from its surrounding floodplain, which further increases the rates of incision, streambed mobility, and scour depth.  Another effect of incision has been a significant reduction in large woody debris input to Lagunitas Creek and its tributaries, which also greatly diminishes the capacity for these creeks to store, sort, and meter sediment. 

Habitat conditions are degraded by elevated concentrations of fine sediment in the streambed (primarily sand) - caused by pervasive alteration of sediment supply, transport, and storage - which further reduces juvenile salmonid growth and survival in all freshwater life stages. As sediment supply increases or becomes finer, the streambed can respond by becoming finer and more mobile, as has been documented in tributaries to Lagunitas Creek. Streambed scour at spawning redds can be a significant source of mortality during incubation for coho salmon.

7.3.3.2         Numeric Targets

Increased rate and fining of the bed material supply, channel incision, and a reduction in the number and size of large fallen trees in channels, have all contributed to high to very high rates of streambed mobility and scour in tributaries to Lagunitas Creek that provide important spawning habitat for coho salmon and steelhead, including Arroyo, Cheda, and San Geronimo creeks, and Devils Gulch.  To restore properly functioning conditions, we call for actions to substantially reduce sand supply to Lagunitas Creek and its tributaries, to substantially increase the amount of large woody debris in channels, and, where safe and feasible, to reconnect the channel to its floodplain.  As such we proposed the following targets for streambed mobility and redd scour.

Meeting the numeric targets listed in Table 7.3.3.1 will allow water quality in Lagunitas Creek and its tributaries to achieve the narrative water quality objectives for sediment, settleable material, and population and community ecology.

7.3.3.3        Sediment Sources

Field inventories conducted throughout the Lagunitas Creek watershed provide credible estimates of the rates and sizes of sediment delivered to channels in the watershed during water years 1983 through 2008. Based on this work, the Water Board concludes:

1. Sediment supply to Lagunitas Creek was greater than or equal to two times natural background.  Hillslope erosion processes, considered together with road-related erosion, accounted for about 40 percent of sediment delivery to Lagunitas Creek.  Human-caused channel incision and associated bank erosion, primarily the result of historical land-use disturbances, accounted for about 60 percent of the supply.
2. Rates of sediment supply to channels in the Lagunitas Creek watershed varied substantially, from less than 100 to about 400 metric tons per km2 per year.  Variability is a function primarily of the location of dams, large alluvial valleys (where channels have become deeply incised), road density, and bedrock geology. 
3. Channel incision rates were highest in headwater channel reaches, but incision also was active further downstream (at somewhat lower rates) in the reaches that provide habitat for anadromous salmonids and California freshwater shrimp. 
4. Considering the significant exposure of hard bedrock in the streambed along San Geronimo Creek, and in the mainstem of Lagunitas Creek in the Shafter and State Park reaches, it is unlikely that streambed elevation will become much lower in these reaches.  Absent intervention, complex habitat that now includes riffles and bars will likely decrease, and bedrock exposure will increase, which would further impair habitat condition.
5. While the primary driver for incision is a reduction in large woody debris loading, reduction in coarse sediment supply, following construction of Kent Lake and Nicasio Reservoir, and other historical and ongoing land-use activities also are factors.

In summary, the net result is an elevated amount of fine sediment in the streambed and substantial simplification of channel habitat structure.

The total sediment load in Lagunitas Creek is estimated to have been about 230 percent of natural background upstream of Devils Gulch and about 200 percent of natural background upstream of Olema Creek during the study period. Tables 7.3.3.2 and 7.3.3.3 break down the sediment sources to Lagunitas Creek based on an annual average rate.

7.3.3.4        Total Maximum Daily Load and Allocations

The sediment TMDL for Lagunitas Creek upstream of Devils Gulch is established at 7,500 metric tons per year, which corresponds to about 120 percent of natural background load during the water year 1983 through 2008 period. The sediment TMDL for Lagunitas Creek upstream of Olema Creek is established at 11,900 metric tons per year, which corresponds to about 110 percent of natural background load during the water year 1983 through 2008 period.  Natural background load depends upon natural processes and varies significantly.  Therefore, these TMDLs and associated allocations are expressed both in terms of sediment mass and percent of natural background.  Sediment delivery needs to be reduced overall by about 50 percent from the current proportion of the total load to achieve these TMDLs. Tables 7.3.3.4, 7.3.3.5 and 7.3.3.6 contain the allocations for all sources of sediment in the watershed.

TMDL attainment will be evaluated: a) immediately upstream of the confluence of Lagunitas Creek with Devils Gulch, which approximates the mid-point along the primary spawning reach for coho salmon on Lagunitas Creek; and b) immediately upstream of the confluence of Lagunitas Creek with Olema Creek, which corresponds to the downstream boundary of the TMDL project area. Attainment of the TMDL will be evaluated over a 5-to-10-year averaging period.

7.3.3.5        Implementation Plan

The actions described below, including those to control sediment discharges and enhance stream-riparian habitat complexity and connectivity, are to attain allocations and achieve numeric targets for sedimentation and habitat condition.

Regulatory Tools

The only known point sources of sediment are very small and associated with municipal and construction stormwater runoff, which are regulated under existing NPDES permits that include requirements to control erosion, sedimentation, and hydromodification. Table 7.3.3.7 shows implementation measures required of these sources. The State’s Policy for Implementation and Enforcement of the Nonpoint Source Pollution Control Program requires regulation of nonpoint source discharges using the Water Board’s administrative permitting authorities, including waste discharge requirements (WDRs), waiver of WDRs, Basin Plan Discharge Prohibitions, or some combination of these.  Consistent with this policy, Tables 7.3.3.8, 7.3.3.9, and 7.3.3.10 specify actions and performance standards by nonpoint source category to achieve TMDL sediment targets and allocations in the Lagunitas Creek watershed.

Control of Nonpoint Sources of Sediment

The only significant nonpoint source that is not effectively controlled through existing programs and/or natural recovery processes is sediment discharge from roads. This gap applies only to publicly-owned roads, primarily unpaved roads under the jurisdiction of the State Department of Parks and Recreation in S.P. Taylor State Park and/or the U.S. National Park Service within the Golden Gate National Recreation Area. Paved public roads, almost all under the jurisdiction of the County of Marin, also may contribute significant amounts of sediment to channels, although at lower rates.

With regard to the unpaved public roads, reasonable assurances are in place through a memorandum of understanding (MOU) - for the maintenance and management of unpaved roads – that has been agreed to by all of the public agencies within the project area with jurisdiction over roads.  Through this MOU, substantial progress has been made to control and reduce sediment delivery to channels. The Marin Open Space District and the Marin Municipal Water District already achieve the performance standard for unpaved roads under their jurisdiction in the Lagunitas Creek watershed.

To ensure that effective sediment source controls are implemented on all public roads –unpaved and paved - consistent with the State Nonpoint Source Program, WDRs, or a conditional waiver of WDRs, are required to meet the road sediment delivery performance standard (Table 7.3.3.9). Whether through adoption of a conditional waiver of WDRs or adoption of WDRs, the required actions are as follows:

• The County of Marin, Department of Public Works, within five years of TMDL adoption, must conduct an inventory of its paved roads within the project area to identify sediment delivery sites and produce a schedule for treatment, as needed, to achieve road sediment delivery performance standards listed in Table 7.3.3.9.
• The State Department of Parks and Recreation within S.P. Taylor State Park and the U.S. National Park Service, within that portion of the Golden Gate National Recreation Area that is in the TMDL project area, must control sediment delivery sites on unpaved roads to achieve the performance standard for road-related sediment delivery (Table 7.3.3.9). 
• All public agencies with jurisdiction over roads within the project area must adopt and implement road maintenance guidelines to protect aquatic habitat, water quality, and salmonid fisheries; conduct a biennial training program for road maintenance staff, and biennially submit a report that documents implementation and/or recommends adaptive updates to the maintenance practices.

Actions to Enhance Stream-Riparian Habitat Complexity and Connectivity

Although future sediment delivery from channel incision is predicted to decline substantially as a result of natural process adjustments, absent implementation of a habitat enhancement program, stream-riparian habitat condition will remain substantially degraded. Stream habitat degradation in the channel reaches that remain accessible to populations of coho salmon and steelhead is a key factor in their decline.  Floodplains and large woody debris jams provide essential high quality rearing habitats and enhance food production for coho salmon, steelhead, and California freshwater shrimp.  These features also reduce streambed scour and sort, meter, and store fine sediment, thereby substantially enhancing the diversity of streambed substrate patches. Therefore, the primary focus of this Plan is a program of channel habitat enhancement, presented in Table 7.3.3.10, focused on actions to substantially increase the amount of large woody debris in channels and to develop focused technical studies to identify priorities and opportunities for floodplain restoration (in channel reaches where it is safe and feasible to do so). Goals for these actions are presented in Table 7.3.3.11.  Continued implementation of the Memorandum of Understanding for Woody Debris Management in Riparian Areas of the Lagunitas Creek Watershed by the Marin Municipal Water District and other public agencies also will contribute to increased large woody debris loading.

Problems associated with channel incision reflect and integrate multiple historical and ongoing disturbances, some of which are local and direct, and others that are indirect and distal. Effectively addressing these issues will require cooperative and coordinated actions by multiple landowners, working with public agencies, over significant distances along Lagunitas Creek and its tributaries. The Water Board will emphasize cooperative programs to achieve the floodplain restoration and/or large woody debris enhancement goals acting in coordination with the State Water Board Division of Water Rights (Table 7.3.3.11). 

The Water Board also encourages stakeholders along San Geronimo Creek and its tributaries to develop reach-based stewardship groups to implement channel habitat enhancement projects in this part of the watershed.  Public funding for such efforts should be prioritized for reaches where both potential gains in habitat function are significant and necessary landowner support and participation can be achieved. 

Agricultural Water Quality Control Program Costs

Implementation measures for grazing lands and roads located on those same properties constitute an agricultural water quality control program and, therefore, consistent with California Water Code requirements (Section 13141), the cost of this program is estimated herein.  The Tomales Bay watershed pathogens TMDL that was adopted in 2005, which includes all ranches and grazing areas within the Lagunitas Creek watershed, estimates costs to ranch operators to implement best management practices to control pathogen discharges from rangelands including maintaining adequate amounts of residual dry matter in rangelands and the costs of excluding livestock from water courses by construction and maintenance of fences in these sensitive areas.  Those actions also are expected to satisfy performance standards for control of surface erosion in rangelands and control of sediment discharge from unstable areas.  As such, we do not consider these existing costs, associated with compliance with the previously adopted pathogens TMDL, in calculating the agricultural water quality control program costs associated with achieving compliance with the Lagunitas Creek sediment TMDL.  The only new agricultural water quality control program costs are those related to attainment of performance standards and load allocations for sediment discharge from roads to channels.  In the Lagunitas Creek watershed, we estimate that there are 20 miles of roads located on privately owned ranchlands.  In estimating potential cost of compliance, we reference recently completed road erosion inventories conducted on unpaved roads located on ranches and/or parklands in the Lagunitas Creek watershed that include estimates of the costs for treating all significant sediment delivery sources from those roads.  Relying on these data, we estimate that the maximum total cost to ranch operators, assuming no public funding is available to support this work, could cost $420,000 over the 20-year implementation period associated with achievement of the TMDL, or about an average of $21,000 per year.  However, the actual cost to agricultural landowners should be lower because it is reasonable to conclude that some projects will qualify for grant funding from public agencies.

7.3.3.6        Evaluation and Monitoring

Three types of monitoring are specified to assess progress toward achievement of numeric targets and load allocations for sediment:

• Implementation monitoring to document actions to reduce fine sediment discharge and enhance habitat complexity and connectivity;
• Upslope effectiveness monitoring to evaluate effectiveness of sediment control actions in reducing rates of sediment delivery to channels; and
• In-channel effectiveness monitoring (e.g., streambed mobility and redd scour) to evaluate channel response to management actions and natural processes.

Implementation monitoring will be conducted by landowners or designated agents. The purpose of this type of monitoring is to document that sediment control and/or habitat enhancement actions specified herein actually occur.  

The Water Board, working in partnership with other government agencies, plans to conduct upslope effectiveness monitoring.  This will include an update to all or part of the watershed sediment budget, to re-evaluate rates of sediment delivery to channels from land-use activities and natural processes (ten years subsequent to Basin Plan amendment adoption), in the fall of 2024, when sediment delivery associated with land-use activities are projected to be reduced by 25 percent-or-more. 

In-channel effectiveness monitoring should be conducted by local government agencies with scientific expertise and demonstrated capability in working effectively with private property owners (to gain permissions for access), as needed to develop a representative sample of stream habitat conditions, in relation to sediment supply and transport within the watershed. In-channel effectiveness monitoring needs to include measurements of redd scour and streambed mobility to evaluate attainment of water quality objectives for settleable material.  Water Board staff will work collaboratively with local partners to develop and refine the in-channel effectiveness monitoring program.

Streambed mobility (τ*) should be measured in gravel-bedded channel reaches along Lagunitas Creek and in its tributaries where the adjacent valley flat is a floodplain.  

Redd scour should be measured at 30-or-more potential spawning sites, with 4-or-more scour measurements per spawning site, as needed, to establish a high level of statistical confidence in estimated values.  Redd scour sampling sites should be stratified based on estimated average annual sediment supply rate. 

Large woody debris loading in channels also needs to be surveyed and assessed to evaluate attainment of the numeric targets for large woody debris loading and to guide development of reach-specific prescriptions for installation of engineered log jams and riparian management actions to maintain or exceed the target values in future years through natural recruitment. 

Desired measurement frequency for streambed mobility, redd scour, and large woody debris is once every three years.

7.3.3.7        Adaptive Implementation

In concert with the monitoring programs, described above, the Water Board will adapt the Lagunitas Creek Sediment Reduction and Habitat Enhancement Plan and TMDL. In amending the Basin Plan amendment, the Water Board will consider, at a minimum, the results of validation monitoring conducted to confirm or reject hypotheses regarding effects of actions to enhance large woody debris loading and floodplain area on population dynamics of coho salmon, steelhead, and California freshwater shrimp. The Water Board will also consider the results of salmonid population monitoring programs including juvenile population estimates, adult spawner surveys, and smolt outmigration surveys performed to evaluate the status and trends of these populations and also related analyses of smolt population dynamics in response to changes in the quantity and quality of freshwater habitat.  We note that Lagunitas Creek has been identified as a life-cycle monitoring station in the California Department of Fish and Wildlife’s Coastal Monitoring Plan (CMP).  The Lagunitas Creek Sediment TMDL will seek to dovetail with the CMP’s evaluations of salmonid population status and trends in the watershed.

7.4 Water Quality Attainment Strategies and TMDLs for the San Mateo Coastal Basin (see Figure 2-4)

7.4.1 San Pedro Creek and Pacifica State Beach Bacteria TMDL

The following sections establish the TMDL for bacteria in San Pedro Creek and at Pacifica State Beach. The numeric targets, load and wasteload allocations, and implementation plan are designed to support and protect these water bodies’ designated beneficial use of water contact recreation (e.g., swimming and fishing).  

7.4.1.1        Problem Statement

San Pedro Creek and Pacific Ocean waters adjacent to Pacifica State Beach are impaired by bacteria. Bacteriological water quality objectives are exceeded based on elevated indicator bacteria densities, and thus, there is impairment of the water contact recreation (REC-1) beneficial use in these water bodies. Recreating in waters with elevated indicator bacteria densities has long been associated with adverse health effects. Specifically, national epidemiological studies demonstrate that there is a causal relationship between adverse health effects and recreational water quality, as measured by indicator bacteria densities.

7.4.1.2        Sources

Bacteria sources are identified based on the results of a bacterial source tracking study completed in 2009 and from documentation of inadequately treated human waste discharges from Pacifica’s sanitary sewer system. If not properly managed, the following source categories have the potential to discharge bacteria to San Pedro Creek and Pacifica State Beach: sanitary sewer systems, horse facilities, and municipal stormwater runoff and dry weather flows.

7.4.1.3        Numeric Targets

This TMDL establishes a desired, or target, condition for the water contact recreation use in San Pedro Creek and at Pacifica State Beach based on the water quality objectives for indicator bacteria. The numeric targets for San Pedro Creek are based on the Basin Plan water quality objectives for coliform bacteria for water contact recreation use in fresh water (the E.coli targets are the U.S. EPA bacteriological criteria for water contact recreation in fresh waters that are also contained in the Basin Plan). The numeric targets for Pacifica State Beach are based on the Ocean Plan water quality objectives for water contact recreation use in marine waters. The water quality objectives for both marine and freshwater that form the basis of the numeric targets for this TMDL are listed in Table 7.4.1-1.

It is not the intent of this TMDL to require treatment or diversion of water bodies or to otherwise require treatment of natural sources of indicator bacteria. Therefore, for this TMDL, a reference system and antidegradation approach has been incorporated in the numeric targets as an allowable number of times that the water quality objectives can be exceeded. The purpose of the allowable number of exceedances of the water quality objectives is to account for the natural, and largely uncontrollable sources of bacteria (e.g., birds and wildlife feces), which have been shown can, by themselves, cause exceedances of the REC-1 water quality objectives. Hence, the numeric targets for this TMDL are the allowable number of exceedances of the single-sample water quality objectives as listed in Table 7.4.1-2.

The number of allowable exceedances is based on two criteria: (1) bacteriological water quality at any site must be at least as good as at a designated reference system; and (2) there is no degradation of existing bacteriological water quality if historical water quality at a particular site is better than the designated reference system.

The numeric targets based on the allowable exceedances of single-sample objectives are also the bacteria TMDLs and load and wasteload allocations.

7.4.1.4        Total Maximum Daily Loads

The TMDLs for San Pedro Creek and Pacifica State Beach are the same as the numeric targets listed in Table 7.4.1-2 and are expressed in terms of allowable exceedances of single-sample objectives.

7.4.1.5        Load and Wasteload Allocations

Load allocations and wasteload allocations are the same as the numeric targets and TMDLs listed in Table 7.4.1-2 and are expressed in terms of allowable exceedances of single-sample objectives. Table 7.4.1-3 summarizes the allocations for discharges of bacteria in the San Pedro Creek watershed. Dischargers that discharge to San Pedro Creek have allocations based on allowable exceedances for San Pedro Creek. Dischargers that discharge to Pacifica State Beach have allocations based on allowable exceedances for Pacifica State Beach. The TMDLs, load allocations, and wasteload allocations for Pacifica State Beach shall be attained within 8 years of the effective date of the TMDL. The TMDLs, load allocations, and wasteload allocations for San Pedro Creek shall be attained within 15 years of the effective date of the TMDL.  

All entities that discharge indicator bacteria or have jurisdiction over such dischargers are collectively responsible for meeting these allocations. Dischargers shall demonstrate achievement of allocations in the receiving water bodies (i.e., at the mouth of San Pedro Creek and at the existing San Mateo County shoreline water quality monitoring station #5 at the Pacifica State Beach).

7.4.1.6        Implementation Plan

The San Pedro Creek and Pacifica State Beach Bacteria TMDL implementation plan specifies actions needed to attain the TMDL and allocations. The implementation plan includes actions for which requirements are already in place, and some additional new actions. The new actions include requirements for horse facility owners and operators to obtain coverage under waste discharge requirements to ensure the clean operation of their facilities; and new requirements for stormwater management. Actions for which requirements are already in place, as of the TMDL effective date, include: 1) reduction of sanitary sewer discharges by the measures required under an existing Cease and Desist Order issued to the City of Pacifica and the general waste discharge requirements for sanitary sewer systems; and 2) a Cleanup and Abatement Order issued to one of the horse facilities in the watershed. 

The required implementation actions are consistent with the following existing regulations and Orders:

Water Board Orders and Discharge Prohibition

• Statewide General Waste Discharge Requirements for Sanitary Sewer Systems (Order No. 2006-0003-DWQ)
• Statewide Construction Stormwater NPDES General Permit (Order No. 2009-0009-DWQ; NPDES Permit No. CAS000002)
• Municipal Regional Stormwater NPDES Permit (Order No. R2-2009-0074 and amendment Order No. R2-2011-0083; NPDES Permit No. CAS612008)
• General Waste Discharge Requirements for Confined Animal Facilities (Order No. R2-2003-0093)
• Basin Plan Discharge Prohibition No. 15 (Table 4.1), which states: “it shall be prohibited to discharge raw sewage or any waste failing to meet waste discharge requirements to any waters of the Basin.”

Water Board Enforcement Orders

• Cease and Desist Order for Pacifica’s Wastewater Discharges (Order No. R2-2011-0031)
• Cleanup and Abatement Order for Millwood Ranch (Order No. R2-2009-0045)

Local Regulations

• San Mateo County Confined Animal Ordinance (Section 7700)
• City of Pacifica Administrative Policy on “Standards for Keeping Animals”
• City of Pacifica Municipal Code for Animal Excreta (Section 6-1.301)
• City of Pacifica Municipal Code for Regulation of Sewer Laterals (Section 6-13.601)

Responsible Parties and Jurisdictions

Wasteload allocations for sanitary sewer systems will be implemented through the requirements and provisions of the Statewide General Waste Discharge Requirements Order for sanitary sewer systems as well as Cease and Desist Order No. R2-2011-0031 issued by the Water Board to Pacifica. Pacifica is the responsible party for implementing these requirements and provisions. 

Load allocations for existing and any new horse facilities will be implemented through the requirements of the Water Board’s General Waste Discharge Requirements for Confined Animal Facilities. The owners of the three horse facilities within the San Pedro Creek watershed (i.e., Millwood Ranch, Park Pacifica Stables, and Shamrock Ranch Stables), as well as any new horse facilities within the watershed, must obtain coverage under and comply with requirements of the updated or existing General Waste Discharge Requirements for Confined Animal Facilities.

Wasteload allocations for municipal stormwater runoff and dry weather flows shall be implemented through the Municipal Regional Stormwater NDPES Permit, or a new stormwater NPDES permit, issued to Pacifica and San Mateo County. No later than six months prior to the expiration date of each NPDES permit, Pacifica and San Mateo County shall submit a plan to the Water Board that describes best management practices (BMPs) that are currently being implemented and the current level of implementation, and additional BMPs that will be implemented, and or an increased level of implementation of existing BMPs, to prevent or reduce discharges of bacteria from their storm drain systems that cause or contribute to exceedance of wasteload allocations. The plan shall include an implementation schedule to account for BMP implementation, and if necessary, trigger implementation of additional BMPs or increased level of implementation, to attain wasteload allocations.

The Water Board may establish permit requirements to implement wasteload allocations based on implementation of BMPs in lieu of numeric limits. The wasteload allocations are not designed to be implemented directly as numeric effluent limitations applicable to a discharger, Pacifica, or San Mateo County. The Water Board will not include numeric limits, based on the wasteload allocations, in NPDES permits if the discharger demonstrates that it has fully implemented technically feasible, effective, and cost efficient BMPs to control all controllable sources to and discharges from their storm drain systems.

Stormwater discharges from the California Department of Transportation’s (Caltrans’) stretch of Highway 1 crossing the northwestern edge of the San Pedro Creek watershed are not a significant source of indicator bacteria because that section of the highway does not include any typical bacteria-generating sources such as homeless encampments, restroom facilities, garbage bins, etc. Caltrans’ existing BMPs and stormwater NPDES permit requirements, as of the effective date of the TMDL, are sufficient to attain and maintain its portion of the wasteload allocation.

Table 7.4.1-4 lists the implementation actions for each of the source categories and the   phased implementation schedule. The implementation schedule allows time for the responsible parties to identify and implement measures that are necessary to control bacteria discharges resulting in exceedances of allocations.

7.4.1.7        Water Quality Monitoring in San Pedro Creek and at Pacifica State Beach

Pacifica and San Mateo County shall, jointly or individually, develop and implement a comprehensive monitoring plan to 1) better characterize indicator bacteria contributions from their source; and 2) assess compliance with wasteload allocations. The monitoring plan shall include applicable bacteria water quality objectives and the sampling frequency shall be adequate to assess compliance with the 30-day geometric mean objectives. Responsible parties may build upon existing monitoring program(s) for San Pedro Creek and Pacifica State Beach when developing the bacteria water quality monitoring plan. At a minimum, in addition to the existing San Mateo County sampling stations at the mouth of San Pedro Creek and at Pacifica State Beach, which will be used to evaluate achievement of the designated load and wasteload allocations, at least one sampling station shall be located in each creek reach/subwatershed, such that bacteria contributions from each of the San Pedro Creek’s forks/subwatersheds are distinguished. In addition, indicator bacteria concentrations in the stormwater and dry weather discharges from the Linda Mar and Anza pump stations shall be monitored and characterized sufficient to determine their contribution to exceedances and the effects of any corrective actions. Lastly, monitoring of some of the stormwater outfalls within the watershed may be needed to characterize and identify indicator bacteria loadings from different land uses and locations and the effects of any corrective actions. Monitoring data shall be entered into the State Water Board’s “Beach Watch” database as appropriate.

7.4.1.8        Adaptive Implementation

The Water Board will adapt the TMDL and implementation plan to incorporate new and relevant scientific information such that effective and efficient measures can be taken to achieve the allocations. The Water Board staff will periodically, in coordination with the implementation schedule, at 5, 8 and 15 years, evaluate new and relevant information from implementation actions, water quality monitoring results and the scientific literature, including any local reference system studies, U.S. EPA’s revised recommended bacteria criteria, or new or revised State bacteria water quality objectives, and assess progress toward attaining TMDL targets and load allocations, and present that information to the Water Board. The Water Board will consider a Basin Plan amendment that reflects any necessary modifications to the targets or implementation plan.

7.4.2 Pescadero-Butano Watershed Sediment TMDL and Habitat Enhancement Plan

This sediment TMDL and habitat enhancement plan address the impairments to beneficial uses in Pescadero and Butano creeks. The following sections establish:

• The sediment TMDL, which identifies the allowable annual sediment load that can be discharged into the Pescadero-Butano watershed, expressed as a percentage of the natural background sediment delivery rate to channels; and
• An implementation plan to achieve the TMDL and habitat enhancement goals.

The goals of the Pescadero-Butano Watershed Sediment TMDL and Habitat Enhancement Plan are as follows:

• To restore water quality and attain beneficial uses.
• To conserve the steelhead trout population.
• To restore a self-sustaining coho salmon population.
• To improve water quality and habitat for native fish and aquatic wildlife species communities.

The TMDL and the implementation plan address the significant increases in sediment supply to channels, as well as simplification, loss, and/or reduction in the quality and quantity of instream habitat for listed populations of salmonids in the Pescadero-Butano watershed. To attain water quality objectives and restore properly functioning channels and habitat, the TMDL calls for actions throughout the watershed to substantially reduce sediment supply to channels and, where safe and feasible, reconnect the channels to their floodplains and enhance channel complexity by adding and retaining large woody debris in channels.

This TMDL focuses on the implementation actions within the channel network upstream of the Pescadero lagoon and marsh complex, located at the watershed-ocean interface, and does not address other water quality issues specific to the Pescadero lagoon and marsh complex. However, achievement of this TMDL is a necessary step to help restore water quality and beneficial uses throughout the watershed, including the lagoon and marsh.

7.4.2.1        Problem Statement

Populations of steelhead and salmon in the Pescadero-Butano watershed have declined substantially over the last century due to progressive changes in land use resulting in excess sediment in the channels and degradation of channel habitat. Land clearing, timber harvesting, legacy grazing and agricultural practices, channel modifications, and roads have: i) increased hillslope erosion; ii) doubled annual sediment supply to channels; iii) resulted in deep incision of Pescadero and Butano creeks and their tributaries; and iv) eliminated sediment storage along the channel and on the floodplains.

Pescadero and Butano creeks are impaired by excess erosion and sedimentation such that the narrative water quality objectives for sediment and settleable material are not being met, and cold freshwater habitat, wildlife habitat, fish spawning and migration,contact and non-contact recreation, and preservation of rare and endangered species beneficial uses are impaired. In addition, the narrative water quality objective for population and community ecology is not being met due to channel incision, which is a significant sediment source and results in habitat simplification and floodplain disconnection. Channel incision and associated simplification of habitat are primary causes of the decline of coho salmon and steelhead trout populations and are controllable water quality factors.

Habitat conditions are degraded by elevated concentrations of fine sediment in the streambed (primarily sand) – caused by pervasive alteration of sediment supply, transport, and storage, which further reduces juvenile salmonid growth and survival in all freshwater life stages. Excess amounts of fine sediment have been deposited on the streambed at potential steelhead spawning and rearing sites. Excess fine sediment in the streambed can cause poor incubation for fish eggs, resulting in high mortality prior to emergence. Fine sediment has also compromised the quality of pools as rearing habitat and reduced winter rearing habitat by filling the spaces between cobbles and boulders.  

Channel incision has severely impacted the basic physical habitat structure of the channel and has caused habitat simplification expressed by a substantial reduction in the frequency and area of gravel bars, riffles, and side channels. Channel incision has isolated channels from their floodplains: floodplains no longer function as sediment storage sites and are lost as excellent rearing and refuge habitats for juvenile salmon and steelhead. In addition, a substantial reduction in the amount of large woody debris in channels has greatly diminished the capacity for the creeks to store, sort, and meter sediment, as well as the quality and diversity of freshwater channel habitats. Lastly, significant and persistent increases in sediment supply and loss of floodplains have contributed to an order-of-magnitude increase in the sedimentation rate in the Pescadero lagoon and marsh, adversely impacting water quality.

7.4.2.2        Numeric Targets

The numeric targets for the TMDL to achieve the Basin Plan’s water quality objectives for sediment, settleable material, and population and community ecology are listed in Table 7.4.2-1.

7.4.2.3        Sediment Sources

Field inventories and sediment modeling conducted throughout the Pescadero-Butano watershed provide credible estimates of the average rate of sediment delivery to channels between 1970 and 2010. Based on this work (Table 7.4.2-2), the Water Board concludes:

1. Sediment delivery to fish-bearing channels has doubled in the last 150 years as compared to the natural background rate. More than half of the fine sediment delivered to Pescadero and Butano creeks and their tributaries is associated with land use activities, including roads, human-caused channel incision, and legacy effects of intensive historical livestock grazing and timber harvesting.
2. The average annual rate of sediment supply to channels in the watershed is 1,200 tons per km² per year.
3. More than 40,000 tons of sediment that historically deposited annually on floodplains and alluvial valley (one third of the total sediment delivered from the watershed) is now transported downstream to the Pescadero lagoon and marsh complex due to channel incision. Therefore, not only has this significant storage function along the floodplains and alluvial valley been lost, but the valley itself is now a significant sediment source. 
4. Contributions of sediment from municipal and construction stormwater runoff are small in comparison to other sources and are estimated to be about 500 tons per year.

7.4.2.4        Total Maximum Daily Load and Allocations

The Pescadero-Butano watershed sediment TMDL is 150,000 tons per year, or 125 percent of the estimated natural background load and applies to Pescadero and Butano creeks and their tributaries. In order to achieve the TMDL, controllable sediment delivery resulting from human actions needs to be reduced by approximately 78 percent (Table 7.4.2-3).

Attainment of the TMDL will be evaluated immediately downstream of the confluence of Pescadero and Butano creeks at the upstream boundary of the Pescadero marsh and lagoon complex. Attainment of the TMDL will be evaluated using a 10-year averaging period.

7.4.2.5        Implementation Plan

The actions described below are necessary to achieve TMDL targets, allocations, performance standards, and habitat enhancement goals within twenty years of the effective date of the Basin Plan amendment.

Stormwater Runoff

Stormwater runoff from State highways and municipal and construction stormwater runoff are the only known point sources of sediment to the Pescadero-Butano watershed and have small wasteload allocations (Table 7.4.2-4) relative to nonpoint sources of sediment. These sources are regulated under existing NPDES permits that include requirements to control erosion, sedimentation, and hydromodification from new development and requirements to maintain rural roads. Table 7.4.2-5 shows implementation measures required for these sources. Implementation to address reductions in loading for sediment discharges associated with roads under the jurisdiction of San Mateo County are included here.

Nonpoint Sources

The State’s 2004 Policy for Implementation and Enforcement of the Nonpoint Source Pollution Control Program provides for regulation of nonpoint source discharges using the Water Board’s administrative permitting authorities, including WDRs, waiver of WDRs, Basin Plan Discharge Prohibitions, or some combination of these. Consistent with this policy, Tables 7.4.2-6, 7.4.2-7, 7.4.2-8, 7.4.2-9, 7.4.2-10, and 7.4.2-11 specify actions and performance standards by nonpoint source category, as needed to achieve TMDL targets and allocations in the Pescadero-Butano watershed. The Water Board will consider adopting permits that apply to the nonpoint sources from roads, grazing lands, non-grazing agricultural lands, and/or timberlands listed in Tables 7.4.2-6, 7.4.2-7, 7.4.2-8, 7.4.2-9, and 7.4.2-10. Individual landowners or coalitions may work with “third parties,” such as the San Mateo Resource Conservation District, to develop and implement sediment pollutant control programs.

Habitat Enhancement

Channel incision, loss of sediment storage function, and loss of essential habitat features are the result of multiple historical and ongoing disturbances. This implementation plan calls for habitat enhancement actions. A channel and habitat restoration program that increases woody debris and re-establishes width-to-depth ratios and a modest flood plain will be the most effective means of controlling channel incision and reducing related sediment delivery to the creeks. Floodplains and large woody debris jams would provide essential high-quality rearing habitats and enhance food production for coho salmon and steelhead. These features also help create pools, reduce scouring, store sediment, and diversify habitat types within the stream. The habitat enhancement program, presented in Table 7.4.2-11, will therefore focus on actions to: (1) to the extent safe and feasible, substantially increase the amount of large woody debris in channels that run through public lands and timber harvest lands; and (2) study safe and feasible opportunities for floodplain restoration in channel reaches on private lands. The effectiveness of implementation of actions specified in Table 7.4.2-11 to enhance habitat will be evaluated as part of the adaptive implementation program.

7.4.2.6        Agricultural Water Quality Program Costs

The implementation measures in Tables 7.4.2-6 and 7.4.2-7 for grazing and agricultural land constitute an agricultural water quality control program and therefore, consistent with Water Code section 13141, the cost of this program is estimated herein. This cost estimate includes the cost of implementing all road-related and surface erosion-related sediment control measures specified in the implementation plan and is based on costs associated with technical assistance, project design, and igmplementation of actions needed to achieve the TMDL.

There are no other costs to farmers or ranchers associated with actions to enhance channel habitat complexity and floodplain connection, because participation by private landowners is voluntary, and almost all of the costs of these projects are expected to be paid for from grants by public agencies and/or non-profits. In estimating costs, the Water Board estimated that owners of grazing and non-grazing agricultural businesses own up to 20 percent of the total land area. The Water Board estimates that the total cost to agricultural businesses associated with efforts to reduce sediment supply to Pescadero and Butano creeks watershed is $200,000 to $300,000 per year.

7.4.2.7        Evaluation and Monitoring

Water Board staff, working in partnership with other entities, e.g., San Mateo County and the San Mateo County Resource Conservation District, will conduct baseline monitoring to document existing residual pool volumes (V*), substrate composition, and woody debris loadings along representative reaches. In addition to baseline conditions monitoring, the following monitoring is necessary:

• Implementation monitoring to document actions taken on individual properties to reduce fine sediment discharge and enhance habitat complexity and connectivity;
• Upslope effectiveness monitoring to evaluate effectiveness of sediment control actions in reducing rates of sediment delivery to channels on a subwatershed basis; and
• In-channel effectiveness monitoring (e.g., pool filling and substrate composition) to evaluate channel response to management actions and natural processes.

Implementation monitoring will be conducted by landowners or designated agents to document that sediment control actions, i.e., best management practices as specified herein, occur. 

The Water Board anticipates working in partnership with the implementing parties to conduct upslope effectiveness monitoring to reevaluate rates of sediment delivered to channels from land use activities and natural processes.

In-channel effectiveness monitoring should be conducted by the Water Board and local partners with scientific expertise and demonstrated capability in working effectively with private property owners (to gain permissions for access), as needed to develop a representative sample of stream habitat conditions, in relation to sediment supply and transport within the watershed. In-channel effectiveness monitoring is needed to evaluate: a) progress toward achieving water quality targets, and b) channel response to management measures and natural processes. The main parameters that will be monitored to assess progress toward achieving water quality targets are residual pool volume and substrate composition.

The Water Board, working in partnership with other entities, such as the San Mateo County Resource Conservation District and other organizations with scientific expertise, will assess large woody debris loading in channels to evaluate attainment of the numeric targets for large woody debris loading and to guide development of reach-specific prescriptions for installation of engineered log jams and riparian management actions to attain the target values in future years through natural recruitment.

Desired measurement frequency for pool filling, substrate composition, and large woody debris is once every five years.

7.4.2.8        Adaptive Implementation

Adaptive implementation entails taking actions commensurate with existing, available information, reviewing new information as it becomes available, and modifying actions as necessary based on the new information. Water Board staff will evaluate and report to the Water Board on the progress of implementation of the TMDL and habitat enhancement actions periodically and will evaluate the need for amending the TMDL within 10 years of the effective date of the TMDL.

Key questions to be considered in the course of adaptive implementation:

• What is the population status of steelhead and coho salmon in the watershed? Do numbers of steelhead and coho salmon increase as sediment reduction and habitat enhancement measures are implemented? An improved understanding of the status of steelhead and salmon populations in the Pescadero-Butano watershed is essential for guiding adaptive updates to the management actions recognized in this plan.
• Are Pescadero and Butano creeks and their tributaries progressing toward TMDL targets and performance standards as expected? If there is a lack of adequate progress, how might the implementation actions, targets, performance standards, or allocations be modified?
• Are the specified sediment reduction measures and recommended habitat enhancement measures resulting in an improving trend in channel habitat quantity and quality?
• Are there new data or information available that warrant revision of water quality targets, allocations, or implementation measures?

7.4.3 TMDL for Beaches in Pillar Point Harbor and Venice Beach

The following sections establish the TMDL for bacteria in Pillar Point Harbor and Venice Beach. The numeric targets, load and wasteload allocations, and Implementation Plan are designed to support and protect the beaches’ designated beneficial use of water contact recreation (e.g., swimming and wading).

7.4.3.1         Problem Statement

Bacteria densities in the waters of the beaches in Pillar Point Harbor and Venice Beach exceed the numeric water quality objectives for Enterococcus, which are types of bacteria that indicate the potential for fecal contamination and an elevated risk of pathogen-induced illness to people. Monitoring data show chronic exceedances of objectives for Enterococcus at multiple beach segments, which has led to health advisories and beach closures. These exceedances and postings threaten and impair the water contact recreation (REC-1) and non-contact water recreation (REC-2) beneficial uses.

7.4.3.2         Sources

If not properly managed, the following sources have the potential to discharge bacteria to the beaches in Pillar Point Harbor and Venice Beach: onsite wastewater treatment systems, sanitary sewer overflows, sewer collection systems, the Sewer Authority Mid-Coastside wastewater treatment plant, Pillar Point Harbor and Marina operations, private sewer laterals, municipal stormwater, runoff from landfills, Caltrans stormwater runoff, horse boarding facilities, grazing and wildlife.

7.4.3.3         Numeric Targets

The desired or target condition for the water contact beneficial use in Pillar Point Harbor beaches and Venice Beach are listed in Table 7.4.3-1. These targets are based on protective water quality objectives for marine (estuarine) waters adopted by the State Water Board in the Water Quality Control Plan for Inland Surface Waters, Enclosed Bays, and Estuaries of California.

7.4.3.4         Total Maximum Daily Load

The TMDL is equivalent to the numeric targets in Table 7.4.3-1. The TMDL is expressed as the total density of Enterococcus indicator bacteria that can be discharged from all sources without causing the water quality at the beaches in Pillar Point Harbor and Venice Beach to exceed the protective standards. The daily load expression of this TMDL is equivalent to the statistical threshold value of 110 cfu/100mL) for Enterococcus. The TMDL is applicable year-round.

7.4.3.5         Load and Wasteload Allocations

Table 7.4.3-2 summarizes the allocations for discharges of bacteria. The load allocations (LAs) and wasteload allocations (WLAs) are the same as the numeric targets specified in Table 7.4.3-1 and the TMDL, except that the allocation for onsite wastewater treatment systems, sanitary sewer collection systems, and marina vessels and harbor amenities is zero. The allocations are expressed in terms of Enterococcus densities. The daily load expression of the WLAs and LAs in Table 7.4.3-2 is equivalent to the appropriate STV, unless the discharge of bacteria is prohibited then the allocation is zero.

All entities that discharge indicator bacteria or have jurisdiction over such discharges are responsible for meeting these allocations. Implementing parties shall demonstrate achievement of allocations in the receiving water bodies (i.e., at the beach shoreline water quality monitoring stations). The attainment of these allocations will ensure protection of water quality and the applicable beneficial uses at the beaches. All LAs and WLAs shall be achieved for each implementing party no later than 15 years after the TMDL effective date. Successfully completing corrective action to reduce or eliminate a discharge from a particular source, as called for in the Implementation Plan, may be used to show that the corresponding source has achieved its LA or WLA.

7.4.3.6         Implementation Plan

The Implementation Plan specifies actions needed to attain the TMDL and allocations. This Implementation Plan builds on management measures required by existing local, regional, and statewide regulations and orders to reduce or eliminate waste discharges from sanitary sewer collection systems, OWTS, confined animal facilities, municipal stormwater runoff, and vessels. Cooperation among implementing parties is encouraged, not only to attain the TMDL but also to avoid duplicative actions, such as monitoring and reporting. To the extent possible, implementing parties should coordinate actions and water quality monitoring efforts.

Regulatory Tools

The Water Board will use its regulatory authorities to require actions in the Implementation Plan, including individual and general WDRs under Water Code section 13263; waivers of WDRs under Water Code section 13269; technical or monitoring program reports under Water Code section 13267; NPDES permits for wastewater discharges from the Sewer Authority Mid-Coastside and collection systems; NPDES permits for the Ox Mountain Landfill; NPDES permits for stormwater discharges from municipal and Caltrans separate storm sewer systems under the Clean Water Act section 402 and Water Code section 13377; and vessel sanitation requirements under the Harbors and Navigation Code section 775 et seq. The Water Board will also use its authorities to implement the State Water Board’s Water Quality Control Policy for Siting, Design, Operation, and Maintenance of Onsite Wastewater Treatment Systems (OWTS Policy). The Water Board may also enforce the Basin Plan’s prohibition of discharges of raw sewage or any waste failing to meet WDRs.

Implementation Actions and Schedule

Tables 7.4.3-3, 7.4.3-4, 7.4.3-5, 7.4.3-6, 7.4.3-7, 7.4.3-8, 7.4.3-9, 7.4.3-10, 7.4.3-11, 7.4.3-12, and 7.4.3-13 show the implementation and monitoring actions, implementing parties, and schedule to achieve the TMDL. The schedule allows time for the implementing parties to identify and implement measures that are necessary to control bacteria discharges resulting in exceedances of allocations. If source control actions are fully implemented throughout the watershed and the TMDL targets are not met, the Water Board may re-evaluate or revise the targets, TMDL, and allocations as appropriate. All implementing parties are required to attain their respective allocations by taking a phased approach in which additional or enhanced actions are required if initial implementation actions do not result in attainment of the TMDL within approximately five years. The Implementation Plan recognizes that early implementation actions, including, for example, mapping and cleaning of stormwater and sewer pipes, catch basin cleaning, and education and outreach campaigns to reduce pet waste in the past five years, are achieving progress toward attaining the TMDL load and wasteload allocations.

7.4.3.7         Water Quality Monitoring

Implementing parties are responsible for developing and implementing a monitoring plan sufficient to assess compliance with the numeric targets at the beaches in Pillar Point Harbor and Venice Beach. At a minimum, implementing parties will continue monitoring the beaches as required under California Health and Safety Code section 115880 and provide a data evaluation report annually to the Water Board. It is recommended that the implementing parties select a lead entity to assess the monitoring data and compile the annual report.

If the TMDL target is not achieved after five years, i.e., following implementation of Phase 1 actions, the implementing parties can delay Phase 2 implementation for up to four years if they conduct or cause to be conducted enhanced bacteria source identification studies. Implementing parties (to include San Mateo County and Harbor District, City of Half Moon Bay, Sewer Authority Mid-Coast, Granada Community Services District and California Parks and Recreation) will be required to contribute to this effort as appropriate and may choose to begin special studies during Phase 1. For example, monitoring catchments within the watershed may help identify and characterize indicator bacteria loadings from different land uses and locations or may evaluate the effectiveness of bacteria control actions. The Water Board will collaborate with implementing parties to investigate any remaining data gaps, including the contribution of natural sources of bacteria to the impairment.

The CAF permittees are required to comply with the monitoring requirements of the Water Board’s CAF Order. However, in lieu of the TMDL fecal indicator bacteria water quality monitoring, CAFs and grazing operations may demonstrate attainment of their LAs through sampling of other indicator parameters (e.g., ammonia) or by demonstrating they have implemented all required implementation measures for addressing bacteria discharges from their respective source categories.

For the OWTS source, the Water Board will track and use proof of required corrective actions taken by the property owners as evidence that they have achieved the LA. No additional water quality monitoring is required for this source to demonstrate attainment of the LA.

The Ox Mountain Sanitary Landfill shall monitor the indicator bacteria concentrations in the receiving water to demonstrate that their WLA is met.

7.5 Water Quality Attainment Strategies and TMDLs for the Central Basin (see Figure 2-5)

7.5.1 Richardson Bay Pathogens Total Maximum Daily Load (TMDL)

The following sections establish the TMDL for pathogens in Richardson Bay. The numeric targets, load allocations, and implementation plan are designed to support and protect the Bay’s designated beneficial uses, water contact recreation and shellfish harvesting. The TMDL includes actions for adaptive implementation to evaluate the effectiveness of implementation actions, monitor progress toward targets, and review the scientific understanding pertaining to pathogens, which may result in modifying the TMDL in the future.

7.5.1.1    Problem Statement

Richardson Bay is impaired by pathogens. Monitoring results indicate that the Bay exceeds bacteria water quality objectives for shellfish harvesting (e.g., clam, mussel, and oyster harvesting), and water contact recreation (swimming, fishing); Table 3-1). The presence of pathogens is inferred from high concentrations of fecal coliform bacteria, a commonly used indicator of human pathogenic organisms. Therefore, the beneficial uses of shellfish harvesting and recreational water contact are not fully supported.

7.5.1.2    Sources

Pathogen sources are identified based on elevated coliform bacteria (pathogen indicator) levels downstream or in the vicinity of identified land uses or facilities and from documentation of inadequately treated human waste discharges. If not properly managed, the following source categories have the potential to discharge pathogens to Richardson Bay: sanitary sewer systems, stormwater runoff, houseboats, and vessels.

• High coliform levels detected downstream of storm drains, and the increase in the number of wet season exceedances as compared to the number of dry season exceedances, point to stormwater runoff as a potential pathogen source.
  
• Documentation of sanitary sewer overflows in Richardson Bay area municipalities suggests that sanitary sewer systems are a potential source of pathogens to the Bay. 
  
• Consistently high coliform levels in houseboat and vessel marinas indicate that houseboat and vessel marinas’ failing sewage collection systems are potential sources of pathogens.
  

Bacteria levels are low at monitoring sites that contain wildlife but are minimally impacted by human activities. This suggests that wildlife may not be a significant, widespread potential source of pathogens in Richardson Bay. Wildlife may be a significant source on an intermittent, localized basis.

7.5.1.3    Numeric Targets 

The numeric targets (desired future long-term conditions) proposed for pathogen indicators in Richardson Bay are presented in Table 7.5.1-1.

The bacterial density targets are based on the Basin Plan’s shellfish harvesting and water contact recreation water quality objectives for fecal coliform and on U.S. EPA’s recommended Enterococci criteria for water contact recreation in salt water. 

7.5.1.4    Total Maximum Daily Load

Table 7.5.1-2 shows Richardson Bay’s density-based pathogens TMDL, expressed as fecal coliform bacteria concentrations.

7.5.1.5    Load Allocations

Density-based fecal coliform allocations for each potential pathogen source category in Richardson Bay are presented in Table 7.5.1-3. Each discharger in the Richardson Bay watershed is responsible for meeting its source category allocation. All potential dischargers are also responsible for complying with applicable waste discharge requirements, or waste discharge prohibitions (Table 4-1, Prohibitions 5, 15, and 18).

All discharges of raw or inadequately treated human waste, including sewage from vessels, are prohibited. All sources of untreated or inadequately treated human waste have an allocation of zero.

7.5.1.6    Implementation Plan

The Richardson Bay Pathogens TMDL Implementation Plan builds upon previous and ongoing successful efforts to reduce potential pathogen loads in Richardson Bay and its tributaries. The plan requires actions consistent with the California Water Code (CWC 13000 et seq.), the state’s Nonpoint Source Pollution Control Program Plan (CWC Section 13369), the Policy for Implementation and Enforcement of the Nonpoint Source Pollution Control Program, and human waste discharge prohibitions (Table 4-1, Prohibitions 5, 15, and 18).

Table 7.5.1-4 lists the required implementation measures for the source categories listed in Table 7.5.1-3. These measures include evaluation of operating practices, identification of comprehensive, site-specific pathogens control measures and an associated implementation schedule, and submittal of progress reports to the Water Board documenting actions taken.

Regulatory Framework

The state’s Policy for Implementation and Enforcement of the Nonpoint Source Pollution Control Program requires that current and proposed nonpoint source discharges be regulated under waste discharge requirements, waivers of waste discharge requirements, Basin Plan discharge prohibitions, or some combination of these tools. Municipal and highway stormwater runoffs are regulated under NPDES permits. Table 7.5.1-5 describes the regulatory mechanism by which dischargers in each source category will be regulated.

Ongoing Water Quality Monitoring in Richardson Bay

Water quality monitoring will be conducted to assess water quality improvements and obtain additional information for further refinement of the TMDL. The main objectives of the ongoing monitoring program are to:

• Assess attainment of TMDL targets
  
• Evaluate spatial and temporal water quality trends in the Bay
  
• Obtain additional information about significant potential pathogen source areas
  
• Collect sufficient data to prioritize implementation efforts and assess the effectiveness of source control actions
  

All water quality monitoring (including Quality Assurance and Quality Control procedures) will be performed pursuant to the State Water Board’s Quality Assurance Management Plan for the Surface Water Ambient Monitoring Program.

Adaptive Implementation

In 2013, the Water Board will evaluate monitoring results and assess progress toward attaining TMDL targets (Table 7.5.1-1) and load allocations (Table 7.5.1-3). The Water Board will also evaluate compliance with the trackable implementation measures specified in Table 7.5.1-4, as documented by submitted progress reports.

If evaluation and monitoring show that source control actions have been fully implemented throughout the watershed, but the TMDL targets (water quality objectives) are not attained, the Water Board may re-evaluate the attainability/applicability of designated water quality objectives.

The Water Board will review the Richardson Bay Pathogens TMDL and evaluate new and relevant information from monitoring, special studies, and scientific literature. At a minimum, these reviews will aim to find answers to the following questions. Additional questions may be developed in collaboration with stakeholders.

1. Is Richardson Bay progressing toward TMDL targets? If progress is unclear, how can monitoring efforts be modified to detect trends? If there has not been adequate progress, how might the implementation actions be modified?
2. What are the pollutant contributions for the various source categories? How have these contributions changed over time? How do they vary seasonally? How might source control measures be modified to improve load reduction? If the answers to these questions are not clear, how can monitoring efforts be modified to answer these questions? 
3. Is there new, reliable, and widely accepted scientific information that suggests modifications to targets, or implementation actions? If so, how should the TMDL be modified?

Modifications to the targets or implementation plan will be incorporated into the Basin Plan via an amendment process.

7.6 Water Quality Attainment Strategies and TMDLs for the South Bay Basin (see Figure 2-6)

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7.7 Water Quality Attainment Strategies and TMDLs for the Santa Clara Basin (see Figure 2-7)

7.7.1 Total Maximum Daily Loads for Mercury in Waters of the Guadalupe River Watershed

The following sections establish TMDLs for mercury in impaired waters of the Guadalupe River watershed. These TMDLs and associated allocations implement the mercury water quality objectives in waters of the Guadalupe River watershed listed in Table 3-4A.

These TMDLs address seven mercury-impaired waters: five waters on the 2006 303(d) list of impaired waters, Guadalupe Reservoir, Calero Reservoir, Guadalupe Creek, Alamitos Creek, and the Guadalupe River upstream of tidal influence; and two additional waters, Almaden Reservoir and Lake Almaden, which are also impaired by mercury.

These TMDLs are closely integrated with the San Francisco Bay mercury TMDL, which addresses the lower portion of the watershed (from tidal influence to open Bay water, including the Guadalupe River below about Highway 237, both Guadalupe and Alviso sloughs, and the former salt ponds adjacent to these sloughs). Implementation actions in the Guadalupe River watershed TMDLs implementation plan implement the legacy mercury allocation of the San Francisco Bay mercury TMDL to the Guadalupe River watershed.

7.7.1.1    Problem Statement

Fish downstream of the New Almaden Mining District have extremely high concentrations of mercury in their tissues. As of 2004, Guadalupe Reservoir had the highest recorded fish mercury concentrations in California—about 20 times higher than the U.S. EPA methylmercury criterion. To protect the health of humans who consume fish that may be contaminated by mercury, in 1987 Santa Clara County issued a fish consumption advisory warning people not to eat any fish from Guadalupe, Almaden and Calero reservoirs, Guadalupe and Alamitos creeks, the Guadalupe River, and percolation ponds along the river and creeks.

Terrestrial wildlife that primarily or exclusively eat fish (such as piscivorous birds, the most sensitive wildlife species in the watershed) are at risk from mercury. Because mercury concentrations in fish in waters downstream of the New Almaden Mining District exceed both the narrative bioaccumulation objective (see Section 3.3.21) and the numeric aquatic organism and wildlife mercury water quality objectives (Table 3-4A) the health of piscivorous birds is threatened. Beneficial uses of waters in the watershed that are impaired by mercury are water contact recreation (due to human consumption of fish), wildlife habitat, and preservation of rare and endangered species.

7.7.1.2    Sources

Mercury mining waste is the largest source of mercury to waters of the Guadalupe River watershed and San Francisco Bay. Mercury is a legacy pollutant from the California Gold Rush, when cinnabar mines in the Central Coast Ranges produced the mercury used to extract gold from the Sierra Nevada. The world’s fifth-largest mercury mine was the historic New Almaden Mercury Mining District, located in the headwaters of the Guadalupe River watershed.

Current sources of mercury in the Guadalupe River watershed include 1) mercury mining waste, 2) reservoirs, lakes, and shallow impoundments, where mercury is converted to methylmercury, 3) urban stormwater runoff, 4) nonurban stormwater runoff, and 5) atmospheric deposition.

1) Mercury mining waste

Mercury mining waste is found at historic mine sites and downstream of them, at three categories of locations:

a) New Almaden Mining District and Guadalupe Mine. The New Almaden Mining District includes the following mines and their associated processing areas and mining wastes:

New Almaden Mine (Mine Hill, Cora Blanca, Harry, Velasco, Central stope, Victoria, North Randol, South Randol, San Francisco, Santa Mariana, and San Pedro-Almaden mines) America Mine

Providencia Mine Enriquita Mine San Antonio Mine San Mateo Mine Senador Mine Deep Gulch placer cinnabar deposit

Guadalupe Mine is located on Los Capitancillos Ridge contiguous with the New Almaden Mining District, but because of separate ownership, it has retained a distinct name. Because mining waste was not contained on these mine sites, the wastes continue to erode and discharge large quantities of mercury-laden sediments to streams in the watershed.

b) Santa Teresa and Bernal mercury mines. These much smaller, less productive mercury mines are located within the Guadalupe River watershed outside of the New Almaden Mining District. These mines include the mine sites, their associated processing areas, and mining wastes.

c) Depositional areas. Depositional areas downstream of mercury mines accumulate mercury mining waste and include creek beds, banks, and floodplains, percolation ponds, and shallow impoundments. Impoundments are slow-moving water bodies that form behind engineered structures and anthropogenic alterations to the landscape that pond water. Depositional areas also accumulate mercury from other sources, such as urban stormwater runoff and atmospheric deposition. Depositional areas discharge mercury mining waste (in the form of mercury-laden sediment) to surface waters during periods of erosive flows.

2) Reservoirs and lakes.

Reservoirs and lakes (deep impoundments) undergo thermal stratification in the dry season. Thermal stratification increases the conversion of inorganic mercury to methylmercury, a bioaccumulative toxin, in the deep, cold waters of a reservoir or lake’s hypolimnion. In the dry season, reservoirs and lakes discharge elevated methylmercury concentrations to downstream waters.

3) Urban stormwater runoff.

Urban stormwater runoff contains mercury from controllable urban sources, such as improperly discarded fluorescent lamps, electrical switches, thermostats, thermometers, and other mercury-containing devices; historical and ongoing industrial activities; and naturally occurring mercury in soil. Mercury in urban stormwater runoff also results in part from atmospheric deposition to the land surface.

4) Nonurban stormwater runoff.

Nonurban stormwater runoff contains mercury from atmospheric deposition to the land surface, and from naturally occurring mercury in soil.

5) Atmospheric deposition.

Mercury emissions from many industrial processes are widely dispersed in the atmosphere and deposit directly on the land and water surface. Mercury deposition from the atmosphere is minimal relative to other loads in the watershed.

7.7.1.3    Targets

The numeric TMDL targets are the fish-tissue water quality objectives from Table 3-4A designed to protect aquatic organisms and wildlife. They are also protective of human health. The targets are:

• 0.05 mg methylmercury per kg fish, average wet weight concentration measured in whole trophic level 3 fish 5–15 cm in length, and
  
• 0.1 mg methylmercury per kg fish, average wet weight concentration measured in
  whole trophic level 3 fish >15–35 cm in length.

7.7.1.4    Total Maximum Daily Loads

The TMDLs, shown in Table 7.7.1-1, are expressed as methylmercury and mercury concentrations in water and sediment.

7.7.1.5    Load and Wasteload Allocations

Concentration-based pollutant allocations by source category, equal to the TMDLs in Table 7.7.1-1, are shown in Table 7.7.1-2.

7.7.1.6    Implementation Plan

This implementation plan:

• Implements these TMDLs, allocations, and the water quality objectives in Table 3-4A
  
• Builds upon past and ongoing successful efforts to reduce mercury loads both in the Guadalupe River watershed and to San Francisco Bay, and anticipates the development of new and innovative methylmercury control methods
  
• Encourages a coordinated watershed approach
  
• Reduces mercury loads in the watershed and simultaneously to the South Bay Salt Pond Restoration Project adjacent to Alviso Slough and to San Francisco Bay
  
• Reduces methylmercury production in the watershed, and reduces the risks from methylmercury exposure to both humans and wildlife.
  

The Guadalupe River watershed mercury TMDLs implementation plan will proceed in two phases, beginning [effective date of the amendment], with targets to be attained before 2029. The goals for the first phase include implementing effective source control measures for mining waste at mine sites; completing studies to reduce discharge of mining waste accumulated in Alamitos Creek; and completing studies of methylmercury and bioaccumulation controls in reservoirs and lakes, by December 31, 2018. The goal for the second 10-year phase of implementation is the attainment of the watershed fish tissue targets and the San Francisco Bay mercury TMDL allocations to urban stormwater runoff and legacy mercury sources in the Guadalupe River watershed, by December 31, 2028.

This plan establishes requirements for responsible parties to reduce or control mercury loads using available technology (see Mercury Source Control Actions). If methods under development to reduce methylmercury production and bioaccumulation prove feasible and effective, this plan also requires responsible parties to implement proven methods in Phase I (see Methylmercury Production Control Actions). Monitoring of mercury loads, mercury and methylmercury concentrations in water and suspended sediments, and bioaccumulation will occur throughout both phases to ensure that mercury and methylmercury levels have declined and fish targets are attained (see Coordinated Watershed Monitoring Program). The adaptive implementation section describes the approach and schedule for evaluating and adapting the TMDLs and implementation plan as needed to assure water quality standards are attained.

Mercury Source Control Actions

Actions are required to control mercury mining waste and urban runoff sources. This section specifies actions required to control discharges from sources to surface waters.

Mercury mining waste control actions are phased so that mercury discharges from upstream will be eliminated or significantly reduced before downstream projects are undertaken. Erosion control actions at mercury mines shall be completed within the first 10 years (Phase 1). Water Code Chapter 5.7 contains a program for public agencies and cooperating private parties, who are not otherwise legally responsible for abandoned mine lands, to reduce the threat to water quality caused by these lands without becoming responsible for completely remediating mining waste from abandoned mines. The Water Board encourages these parties to participate in the program.

Downstream erosion control actions shall be completed within the second 10 years (Phase 2). Implementation actions that reduce loads of mercury mining waste and/or mercury-laden sediment to the waters of the Guadalupe River watershed downstream of dams will also count towards achieving the San Francisco Bay mercury TMDL allocation to legacy mercury sources in the Guadalupe River watershed.

The implementation plan for urban stormwater runoff, nonurban stormwater runoff, and atmospheric deposition source categories is contained in the San Francisco Bay mercury TMDL. Monitoring required in the Bay mercury TMDL for urban stormwater runoff is similar to the monitoring requirements herein. Consequently, the urban stormwater runoff permittees may find it is advantageous to participate in coordinated watershed monitoring. Urban stormwater runoff implementation actions in the Guadalupe River watershed that reduce loads of mercury to San Francisco Bay will also count towards achieving the Guadalupe TMDL allocation to the urban stormwater runoff source.

Implementation Actions for Mercury Mines

The Water Board will implement load allocations for mercury mining waste discharged from the New Almaden Mining District and the Guadalupe, Santa Teresa, and Bernal mercury mines through Water Code §§ 13267 and 13304 orders to compel investigation, clean up and monitoring, as well as through Basin Plan Section 4.21.4 (Mining Program Description) to the extent applicable. Parties responsible for investigation, cleanup, and monitoring include, but are not limited to, current mine site property owners and prior mine owners and/or operators that have caused or permitted, or threaten to cause or permit, mercury to be discharged or deposited where it will probably be discharged into waters of the State and create a condition of pollution or nuisance.  Except for the cleanup and restoration projects at Hacienda Furnace Yard (including immediately adjacent reaches in Alamitos Creek); Mine Hill; San Francisco Open Cut; Senador, Enriquita and San Mateo mines; Jacques Gulch; and Deep Gulch; the Water Board will issue the § 13267 no later than [six months from the effective date] and the § 13304 orders by June 30, 2011.

These orders will collectively require the responsible parties to:

1. Conduct a site investigation evaluating the erosion potential of mercury mining waste and the potential for seeps to discharge mercury from mining waste to surface waters. Submit the site investigation report for review and approval by the Executive Officer within the first two years of Phase 1, but no later than [two years from the effective date].
2. Develop plans and schedules to control mercury mining waste discharges to surface waters. Submit plans and schedules for review and approval by the Executive Officer within 6 months of approval of the investigation report. Implement the approved plans in accordance with the approved schedule.
3. Cleanup and abate discharges of mercury mining waste within the 10-year duration of Phase 1. Submit a cleanup report for review and approval by the Executive Officer no later than December 31, 2018.
4. Monitor to evaluate the following:
   1. effectiveness of erosion control measures
   2. mercury loads discharged annually to waters of the State at the points of discharge
   3. fish bioaccumulation of mercury in waters downstream of the discharge
   4. mercury loads discharged annually to San Francisco Bay, and
   5. answer the questions posed by special study 3b

Alternatively, the responsible parties may participate in a coordinated watershed monitoring program to address above monitoring requirements c) to e); see Coordinated Watershed Monitoring Program. The Water Board may consider waiving or reducing monitoring requirement b), on an individual basis, based on progress on abating discharges of mining waste and participation in an approved coordinated watershed monitoring program.

Implementation Actions for Depositional Areas

The Water Board will implement load allocations to depositional areas, as defined above, in creeks and the Guadalupe River downstream of mercury mines through Clean Water Act § 401 certifications and/or waste discharge requirements to minimize discharge of mercury-laden sediment. Specifically, when projects are proposed in depositional areas that may result in sediment discharges and/or require § 401 certifications, the Water Board will require projects designed for channel stability and implementation of measures to minimize erosion. Additionally, it will impose monitoring and reporting requirements to demonstrate the effectiveness of erosion control measures in floodplains, creek banks, creek beds, and shallow impoundments.

Examples of projects subject to these requirements include riparian habitat restoration and creek bank stability projects by the District and creekside property owners. The District may also propose projects in shallow impoundments, which will be regulated through the existing § 401 certifications and waste discharge requirements for the District’s Stream Maintenance Program. The Water Board will issue § 401 certifications and/or waste discharge requirements to the District for percolation pond operations and maintenance activities unless actions are satisfactorily undertaken on a voluntary basis.

The Water Board’s strategy for Alamitos Creek, which is highly polluted with mercury mining waste, is to encourage a cooperative effort among the District, local agencies, and creekside property owners to undertake a comprehensive creek bank stability and habitat restoration project. The Water Board encourages the District to be the technical lead for this project, and to seek funding for it. The Water Board will identify mercury cleanup as a grant funding priority for the San Francisco Bay Region. Where necessary, the Water Board will invoke its cleanup authority to compel upstream dischargers who initially discharged mercury mining waste into depositional areas, to cleanup and abate mercury mining waste. Creekside property owners are responsible to provide reasonable access to the creek for project studies, construction, and monitoring, and to not take actions on their property that worsen the discharge of mercury mining waste into the creek. The Water Board urges the District and its partners to complete studies by December 31, 2016; submit plans and schedules for review and approval by the Executive Officer by December 31, 2018; and complete and report on the project within the 10-year duration of Phase 2, by December 31, 2028.

Implementation Actions for Urban Stormwater Runoff

The San Francisco Bay mercury TMDL and urban stormwater NPDES permit require control programs for mercury and monitoring (mercury is a pollutant of concern). The stormwater permit allows for a coordinated and collaborative watershed monitoring program. Urban runoff permittees may participate in a coordinated watershed monitoring program to a) determine fish bioaccumulation of mercury in waters downstream of the discharge (“studies aimed at better understanding the fate, transport, and biological uptake of mercury discharged in urban runoff to San Francisco Bay and tidal areas”), and b) determine the loads of mercury discharged annually to San Francisco Bay; see Coordinated Watershed Monitoring Program. Additionally, if the Water Board determines that special study 3b is necessary, urban runoff permittees shall participate in special study 3b during the second 10-year phase of implementation (see “Special Studies” section below), to determine whether urban stormwater runoff contributes to methylmercury production and bioaccumulation. If special study 3b is necessary and it is not undertaken voluntarily, the Water Board will compel permittees and others (see Special Studies) to undertake special study 3b through Water Code § 13267 requirements.

Methylmercury Production Control Actions

The Santa Clara Valley Water District is a leading researcher in methods of controlling methylmercury production and bioaccumulation in reservoirs and lakes. This TMDL project anticipates that before the end of the implementation period (20 years), new methylmercury production controls in reservoirs and lakes will reduce methylmercury bioaccumulation both in the reservoirs and lakes, and downstream. However, if implementation actions in the reservoirs and lakes do not result in attaining targets downstream, the District shall evaluate and test additional methods of controlling methylmercury production and bioaccumulation in shallow impoundments.

Implementation Actions for Reservoirs and Lakes

The District shall voluntarily conduct or cause to be conducted technical studies of methylmercury production and control. As necessary, the Water Board will compel the District to undertake technical studies of methylmercury production and control through Water Code § 13267 requirements. The responsible party for these studies and subsequent implementation actions is the owner and operator of the reservoirs and lakes, the District. Without methylmercury controls, construction and operation of reservoirs and lakes create nuisance conditions and discharges of methylmercury, which pollutes downstream waters.

The District shall continue to operate, maintain and improve the performance of, or replace with newer technology, existing methylmercury controls already in place on Lake Almaden, Almaden Reservoir, and Guadalupe Reservoir.  The District shall install methylmercury controls in Calero Reservoir, if necessary, by December 31, 2017. The District shall report to the Water Board, by December 31 of odd years until directed to stop, on the operation and effectiveness of the methylmercury controls.

Where the Water Board finds it is feasible to reduce methylmercury production and/or bioaccumulation, the Water Board will issue cleanup and abatement orders to the District to undertake actions to reduce fish mercury concentrations to attain the targets.
The Water Code § 13267 requirements and/or cleanup and abatement orders will also require the District to a) determine the loads of mercury discharged annually to waters of the State at the points of discharge, b) monitor mercury in fish tissue, c) determine the loads of mercury discharged annually to San Francisco Bay, and to d) conduct the special studies described in the Monitoring Program below. Alternatively, the District may participate in a coordinated watershed monitoring program to address monitoring requirements b and c, and to address special study 3b); see Coordinated Watershed Monitoring Program. The Water Board may consider waiving or reducing monitoring requirement a), based on participation in an approved coordinated watershed monitoring program.

The Water Board will consider the need to control methylmercury production and bioaccumulation in shallow impoundments in the reviews described below under “Adaptive Implementation.”

Monitoring Program

The monitoring program encompasses:

1. Monitoring to ensure continued effectiveness of erosion control measures to reduce discharges of mercury mining wastes, including mercury-laden sediment (applicable to mercury mines and depositional areas)
2. Monitoring of mercury load at the points of discharge to demonstrate progress in reducing loads (applicable to mercury mines, and reservoirs and lakes)
3. Fish tissue mercury monitoring to assess progress in attaining targets
   (applicable to mercury mines, and reservoirs and lakes)
4. Monitoring of mercury load to San Francisco Bay to assess progress in attaining the legacy and urban stormwater runoff mass load allocations assigned by the Bay mercury TMDL (applicable to mercury mines, urban stormwater runoff, and reservoirs and lakes)
5. Special studies to inform adaptive implementation of these TMDLs
   (applicable to mercury mines, urban stormwater runoff, and reservoirs and lakes)

The Water Board will compel the responsible parties to conduct monitoring through NPDES stormwater permits, Water Code § 13267 requirements, and/or cleanup and abatement orders, as described above, which will require the responsible parties to submit a (individual or coordinated watershed) monitoring plan no later than [one year from the effective date] for review and approval by the Executive Officer. Although the responsible parties are required to satisfy the monitoring requirements individually, the Water Board encourages a coordinated watershed approach particularly for mercury in fish tissue and loads to San Francisco Bay. The Water Board will collaborate with other resource agencies to coordinate fish monitoring, to leverage their expertise and, where possible, to achieve multiple objectives.
Prey fish (i.e., fish that wildlife consume) methylmercury concentrations shall be estimated as a) one hundred percent of the total mercury in eviscerated fish, or b) ninety-five percent of the total mercury in whole fish, or c) a percentage of methylmercury (as total mercury) in fish tissue based on scientific studies and upon approval of the Executive Officer of the Water Board. Large predator fish (i.e., fish that humans consume) methylmercury concentrations shall be estimated as one hundred percent of the total mercury in skinless filet samples. Water quality shall be monitored at the same time and location as fish collection for mercury species, nutrients, and general water quality parameters.

Coordinated Watershed Monitoring Program

The responsible parties may satisfy monitoring requirements 2–5 through a coordinated effort.   Fish mercury monitoring is best undertaken in a coordinated effort, because fish integrate methylmercury over time and space. Monitoring of legacy (i.e., mercury mining waste) and urban stormwater runoff mercury discharges to San Francisco Bay is best undertaken in a coordinated effort, because this load to the Bay is from a combination of sources and responsible parties. The Water Board encourages a coordinated watershed approach to monitoring, and will consider reducing or waiving monitoring requirement 2 (mercury load at the points of discharge), based on progress in implementation and participation in coordinated watershed monitoring. To participate in the coordinated watershed monitoring program, participating parties shall submit a coordinated watershed monitoring plan no later than [one year from the effective date], for review and approval by the Executive Officer.

Special Studies

Additional studies may be needed to provide information to improve understanding of mercury cycling in the watershed, and to verify assumptions used in developing these TMDLs. Results of the studies will inform adaptive implementation of these TMDLs and the implementation plan. The special studies should address the following questions.

1. How do the reservoirs and lakes in the Guadalupe River watershed differ from one another? Factors to consider include, but are not limited to, area of connected wetlands, food web, water chemistry (phosphorus, pH, acid neutralizing capacity, and dissolved organic carbon), water level fluctuations, and infrastructure (outlet structure). Do outlet samples adequately represent hypolimnetic methylmercury concentrations for each reservoir? How significant are these differences?
2. Is it possible to increase the assimilative capacity for methylmercury in reservoirs and lakes? Is it feasible? If it is feasible, will this help to attain the fish tissue targets? How does increasing the assimilative capacity affect the food web: Is the resulting food chain multiplier from large (>15 cm) trophic level 3 (TL3) to large TL4 fish significantly different from 2? If it is significantly different, where and at what frequency should large predator fish (i.e., fish that humans consume) be monitored?

If the monitoring program has not already provided the information to answer these questions, the District shall voluntarily conduct or cause to be conducted studies 1 and 2, or equivalent or alternative studies with prior approval of the Water Board Executive Officer. As necessary, the Water Board will compel the District to undertake these studies in accordance with Water Code § 13267 requirements (see “Implementation Actions for Reservoirs and Lakes”). Completing study 1 within the first five years of Phase 1 (by December 31, 2013), and completing study 2 within the 10-year duration of Phase 1 (by December 31, 2018), would meet the following goal for the first phase of implementation: “completing studies of methylmercury and bioaccumulation controls in reservoirs and lakes”.

3a.  What effect do the reservoir and lake control measures have on methylmercury bioaccumulation downstream? Are the fish targets attained downstream?

3b.  If not, what factors contribute to methylmercury production and bioaccumulation in creeks and rivers? Factors to consider include, but are not limited to, shallow impoundments, excess nutrients, stagnant pools, shade cover, and aquatic vegetation.

If the monitoring program has not already provided the information to answer these questions, the District shall voluntarily conduct or cause to be conducted study 3a, or equivalent or alternative studies with prior approval of the Water Board Executive Officer. As necessary, the Water Board will compel the District to undertake these technical studies in accordance with Water Code § 13267 requirements (see “Implementation Actions for Reservoirs and Lakes”). If the fish targets are not attained downstream by methylmercury controls in the reservoirs and lakes, the District together with the New Almaden Mining District and the Guadalupe, Santa Teresa and Bernal mercury mines responsible parties, and the urban stormwater runoff permittees shall conduct or cause to be conducted study 3b, or equivalent or alternative studies with prior approval of the Water Board Executive Officer, either voluntarily or in accordance with Water Code § 13267 or NPDES stormwater permit requirements (see above). Completing studies 3a and 3b within the first 5 years of Phase 2 (by December 31, 2023) would support the Water Board’s effort to identify whether methylmercury production and bioaccumulation controls are necessary in shallow impoundments, in accordance with the adaptive implementation program.

4. Where the TL3 50–150 mm target is attained, is methylmercury in fish that Forster’s terns consume (fish less than 50 mm in length), at or below 0.05 mg/kg? Where the TL3 >150–350 mm target is attained, is methylmercury in fish that ospreys consume (TL4 >150–350 mm target), at or below 0.20 mg/kg? If these assumptions pertaining to proportional bioaccumulation are not valid for this watershed, what monitoring should be conducted to support a revised water quality objective and target to protect piscivorous wildlife?
5. Where the larger TL3 target is attained (in fish >150–350 mm), is the smaller TL3 target also attained (fish 50–150 mm)? If so, how should the monitoring frequency for the smaller TL3 target be reduced?

If the monitoring program has not already provided the information to answer these questions, the Water Board will conduct studies 4 and 5. Completing study 4 within the 10-year duration of Phase 1 (by December 31, 2018), would provide timely information to support whether the water quality objectives require revision through the adaptive implementation process. The timing for study 5 is contingent upon the effectiveness of methylmercury controls.

Adaptive Implementation

Adaptive implementation entails taking actions commensurate with the existing, available information, reviewing new information as it becomes available, and modifying actions as necessary based on the new information. Taking action allows progress to occur while more and better information is collected and the effectiveness of current actions is evaluated. Accordingly, these TMDLs will be implemented in phases starting with source controls at mine sites so that upstream mercury discharges will be eliminated or significantly reduced before downstream projects are undertaken.

The Water Board will adapt these TMDLs and the implementation plan to incorporate new and relevant scientific information, so that effective and efficient actions can be taken to attain TMDL allocations and targets. The Water Board recognizes that attaining the methylmercury allocation may be especially difficult because of the need for new and innovative control methods. The Water Board staff will present an annual progress report to the Water Board on implementation of the TMDL that includes evaluation of new and relevant information that becomes available through implementation actions, monitoring, special studies, and current scientific literature. Within ten years of the effective date of this TMDL project (by December 31, 2018), the Water Board will consider amending this TMDL project and implementation plan as necessary to ensure attainment of fish targets in a timely manner.

Reviews will be coordinated through the Water Board’s continuing planning program and will provide opportunities for stakeholder participation. Water Board staff will propose modifications to the targets, allocations, implementation plan actions, or the schedule in this Basin Plan amendment. At a minimum, answers to the following questions will be included in the reviews. Water Board staff will develop additional questions in collaboration with stakeholders during each review.

• Is there new, reliable, and widely accepted scientific information that suggests modifications to targets, allocations, or implementation actions? If so, how should this TMDL project be modified?
  
• Is the watershed progressing toward TMDL targets as expected? If progress is unclear, how should monitoring efforts be modified to detect trends? If there has not been adequate progress, how should the implementation actions or allocations be modified?
  
• Does additional sediment, water column, or fish tissue mercury or methylmercury data support our understanding of linkages and food webs in the watershed? Does new data suggest an alternative allocation or implementation strategy?
  
• What are the current pollutant loads from the various sources? Have these loads changed over time? Are they meeting the allocations? How might source control measures be modified to further reduce loads?
  
• Are Water Board strategies to encourage and compel implementation actions effective? If not, how should the Water Board revise its strategies to reach the goal of attaining fish tissue targets within 20 years?
  
• Can the assimilative capacity for mercury in reservoirs and lakes be increased? If so, how can reservoirs and lakes be managed to reduce bioaccumulation? Should the implementation actions or allocations be modified? If so, how?
  
• Are capital projects like the Lower, Downtown, and Upper Guadalupe Flood Control Projects helping to meet TMDL allocations or are these projects causing increasing loads of mercury and methylmercury to the Guadalupe River and San Francisco Bay? If the loads are increased over pre-project conditions, how might the loads be reduced or their effects be mitigated?

7.8 Water Quality Attainment Strategies and TMDLs for the San Pablo Basin (see Figure 2-8)

7.8 1 Sonoma Creek Pathogens Total Maximum Daily Load (TMDL)

Sonoma Creek and its tributaries are impaired by pathogens. The overall goal of this TMDL is to minimize human exposure to waterborne disease-causing pathogens and to protect uses of water for recreational activities such as wading, swimming, fishing, and rafting.

The most common sources of pathogens are wastes from warm-blooded animals, including humans, livestock, domestic pets, and wildlife. The following sections establish a density-based pathogen TMDL for Sonoma Creek and its tributaries, and identify actions and monitoring necessary to implement the TMDL. The TMDL defines allowable density-based bacteria concentrations and prohibits discharge of raw or inadequately treated human waste. The implementation plan specifies actions necessary to protect and restore water contact recreation beneficial uses.

This TMDL strives to achieve a balance that allows ongoing human activities including agriculture and recreation to continue, while restoring and protecting water quality. As outlined in the adaptive implementation section, the effectiveness of implementation actions, results of monitoring to track progress toward targets, and the scientific understanding of pathogens will be reviewed periodically, and the TMDL may be adapted to future conditions as warranted.

In addition to pathogens, both animal and human wastes contain nutrients that in excess pose a threat to aquatic ecosystem beneficial uses; Sonoma Creek is also listed as impaired by excess nutrients. By eliminating the discharge of human waste and controlling the discharge of animal waste, this TMDL will also protect the beneficial uses of the Sonoma Creek watershed’s aquatic ecosystem, such as cold and warm freshwater habitat, and wildlife habitat. Controlling human and animal wastes discharges will also reduce risks from other harmful constituents such as steroids and pharmaceuticals.

7.8.1.1    Problem Statement

Due to the presence of pathogens in Sonoma Creek and its tributaries, the beneficial uses of water contact and noncontact recreation are impaired.  Waterborne pathogens pose a risk to human health. In ambient waters, the presence of human and animal fecal waste and associated pathogens is inferred from high concentrations of fecal coliform and E. coli bacteria. Bacteria levels in Sonoma Creek and its tributaries are higher than the bacteria water quality objectives established to protect people who swim, wade, and fish in these waters (Table 3-1). Consequently, humans who recreate in Sonoma Creek and its tributaries are at risk of contracting waterborne disease.

7.8.1.2    Sources

The following source categories have the potential to discharge pathogens to surface waters in the Sonoma Creek watershed:

• On-site sewage disposal systems (septic systems)
  
• Sanitary sewer systems
  
• Municipal runoff
  
• Grazing lands
  
• Dairies
  
• Municipal wastewater treatment facility
  
• Wildlife
  

Water quality monitoring data indicate that on-site sewage disposal systems are potentially a significant pathogen source to Sonoma Creek downstream of the community of Kenwood.  Municipal runoff and sanitary sewer lines are the primary pathogen sources in the urban areas.  Livestock grazing and dairies are potentially significant pathogen sources in the more rural portions of the watershed.

Discharger monitoring reports from 2001-2005 indicate that the one municipal wastewater treatment facility is not a significant pathogen source. This facility is considered a potential source due to the possibility of spills or treatment system malfunction.

Wildlife are not a significant, widespread pathogen source, as evidenced by low indicator bacteria levels at sites that contain wildlife but are minimally impacted by human activities. Wildlife may be a significant source on a limited, localized basis.

7.8.1.3    Numeric Targets

The numeric water quality targets listed in Table 7.8.1-1 are derived from water quality objectives for coliform bacteria in contact recreational waters, and from U.S. EPA’s bacteriological criteria (Tables 3-1 and 3-2). The last target, “zero discharge of untreated or inadequately treated human waste,” is consistent with Discharge Prohibition 15 (Table 4-1). The zero human waste discharge target is necessary because human waste is a significant source of pathogenic organisms including viruses; and attainment of fecal coliform targets alone may not be sufficient to protect human health. These bacteria targets, in combination with the human waste discharge prohibitions, are the basis for the TMDL and load allocations, and fully protect beneficial uses.

7.8.1.4    Total Maximum Daily Load

The TMDL, as indicated in Table 7.8.1-2, is expressed as density-based total coliform, fecal coliform, and E. coli bacteria limits.

7.8.1.5    Load Allocations

Density-based pollutant allocations for pathogen source categories are presented in Table 7.8.1-3. This table also presents the wasteload allocation for the single municipal wastewater discharger in the watershed, Sonoma Valley County Sanitation District, and for municipal runoff.  Due to the inherent uncertainty in estimating pathogen loading from nonpoint sources and municipal runoff, allocations for these source categories incorporate a 10 percent margin of safety.  Each entity in the watershed is responsible for meeting its source category allocation.  All facilities are also responsible for meeting the requirements of applicable waste discharge requirements, waivers, or prohibitions.

All discharges of raw or inadequately treated human waste are prohibited. All sources of untreated or inadequately treated human waste have an allocation of zero.

Discharging entities will not be held responsible for uncontrollable discharges originating from wildlife. If wildlife contributions are found to be the cause of exceedances, the TMDL targets and allocation scheme will be revisited as part of the adaptive implementation program.

7.8.1.6    Implementation Plan

This implementation plan builds upon previous and ongoing successful efforts to reduce pathogen loads in Sonoma Creek and its tributaries, and requires actions consistent with the California Water Code (CWC Section 13000 et seq.); the state’s Nonpoint Source Pollution Control Program Plan (CWC Section 13369) and its Policy for Implementation and Enforcement of the Nonpoint Source Pollution Control Program; and the human waste discharge prohibition.

Table 7.8.1-4 contains the required implementation measures for each of the source categories listed in Table 7.8.1-3. These measures include evaluation of operating practices: development of comprehensive, site-specific pathogen control measures and a corresponding implementation schedule: and submittal of progress reports documenting actions undertaken. Progress reports may be submitted directly to the Water Board or to third parties if designated. These progress reports will serve as documentation that source reduction measures are being implemented.

It is important to note that the numeric targets and load allocations in the TMDL are not directly enforceable. To demonstrate attainment of applicable allocations, responsible parties must demonstrate that they are in compliance with specified implementation measures and any applicable waste discharge requirements (WDRs) or waiver conditions.

The state’s Policy for Implementation and Enforcement of the Nonpoint Source Pollution Control Program requires that current and proposed nonpoint source discharges be regulated under (WDRs), waiver of WDRs, Basin Plan prohibitions, or some combination of these tools. Table 7.8.1-5 specifies the regulatory framework for each discharger source category.  The Water Board intends to work with stakeholders to develop conditions for waiving WDRs for grazing lands by 2009.

Cost estimate: Agricultural Water Quality Control Program

Because the implementation measures for grazing lands constitute an agricultural water quality control plan, the cost of that program is estimated below, consistent with California Water Code requirements (Section 13141).

The average annual program implementation cost to agricultural dischargers is estimated to range from $35,000 to $134,000 for the next ten years. These costs will be shared by Sonoma Creek watershed grazing land operators (approximately 10). This estimate includes the cost of implementing animal waste control and grazing management measures, and is based on costs associated with technical assistance and evaluation, installation of water troughs, and livestock control fencing along up to 25 percent of streams in grazing lands. Besides fencing, other acceptable methods of managing livestock access to streams are not included in this cost estimate due to variability in costs and site-specific applicability. In addition to private funding, potential sources of financing include federal and state water quality grants and federal agricultural grants.

Evaluation and Monitoring

Beginning in 2011 and approximately every five years thereafter, the Water Board will evaluate site specific, subwatershed-specific, and watershed-wide compliance with the trackable implementation measures specified in Table 7.8.1-4. In evaluating compliance with the trackable implementation measures, the Water Board will consider levels of participation for each source category as well as for individual dischargers (as documented by Water Board staff or third parties).

In addition to the programmatic monitoring described above, Water Board staff, in collaboration with stakeholders, will conduct water quality monitoring to evaluate E. coli concentration trends in Sonoma Creek and its tributaries. Five years after TMDL adoption, the Water Board will evaluate monitoring results and assess progress made toward attaining TMDL targets (Table 7.8.1-1) and load allocations (Table 7.8.1-3).  The main objectives of the Monitoring Program are to:

• Assess attainment of TMDL targets
  
• Evaluate spatial and temporal water quality trends
  
• Further identify significant pathogen source areas
  
• Collect sufficient data to prioritize implementation efforts and assess the effectiveness of source control actions.
  
• Collect sufficient data to evaluate the costs of pathogen source control measures and the existence of other pollutant reduction benefits (e.g., nutrients or sediments), if any.

Table 7.8.1-6 presents locations for baseline water quality monitoring. Each site will be sampled for E. coli ten times each year. Five samples will be collected weekly during one 30-day period in each wet season (November through March) and one 30-day period in each dry season (May through September). All water quality monitoring (including quality assurance and quality control procedures) will be performed pursuant to the State Water Board’s Quality Assurance Management Plan for the Surface Water Ambient Monitoring Program. Additional monitoring will be conducted as needed if funds are available.

If source control actions are fully implemented throughout the watershed and the TMDL targets are not met, the Water Board may consider whether the TMDL targets are attainable, and re-evaluate or revise the TMDL and allocations as appropriate. Alternatively, if the required actions are not implemented or are only partially implemented, the Water Board may consider regulatory or enforcement action against dischargers not in compliance.

Adaptive Implementation

Approximately every five years, the Water Board will review the Sonoma Creek Pathogen TMDL and evaluate new and relevant information from monitoring, special studies, and the scientific literature. At a minimum, the following questions will be used to conduct the reviews.  Additional questions will be developed in collaboration with stakeholders during each review cycle.

• Are the Creek and the tributaries progressing toward TMDL targets as expected? If progress is unclear, how should monitoring efforts be modified to detect trends? If there has not been adequate progress, how might the implementation actions or allocations be modified?
  
• What are the pollutant loads for the various source categories (including naturally occurring background pathogen contributions and the contribution from open space lands), how have these loads changed over time, how do they vary seasonally, and how might source control measures be modified to improve load reduction?
  
• Is there new, reliable, and widely accepted scientific information that suggests modifications to targets, allocations, or implementation actions? If so, how should the TMDL be modified?
  

Reviews will be coordinated through the Water Board’s continuing planning program, with stakeholder participation. Any necessary modifications to the targets, allocations, or implementation plan will be incorporated into the Basin Plan via an amendment process. In evaluating necessary modifications, the Water Board will favor actions that reduce sediment and nutrient loads, pollutants for which the Sonoma Creek watershed is also impaired.

7.8.2 Napa River Pathogens Total Maximum Daily Load (TMDL)

The Napa River and its tributaries are impaired by pathogens. The overall goal of this TMDL is to minimize human exposure to waterborne disease-causing pathogens and to protect uses of water for recreational activities such as wading, swimming, fishing, and rafting.

The most common sources of pathogens are wastes from warm-blooded animals, including humans, livestock, domestic pets, and wildlife. The following sections establish a density-based pathogen TMDL for the Napa River and its tributaries, and identify actions and monitoring necessary to implement the TMDL. The TMDL defines allowable density-based bacteria concentrations and prohibits discharge of raw or inadequately treated human waste. The implementation plan specifies actions necessary to protect and restore water contact recreation beneficial uses.

This TMDL strives to achieve a balance that allows ongoing human activities including agriculture and recreation to continue, while restoring and protecting water quality. As outlined in the adaptive implementation section, the effectiveness of implementation actions, results of monitoring to track progress toward targets, and the scientific understanding of pathogens will be reviewed periodically, and the TMDL may be adapted to future conditions as warranted.

In addition to pathogens, both animal and human wastes contain nutrients that in excess pose a threat to aquatic ecosystem beneficial uses; the Napa River is also listed as impaired by nutrients. By eliminating the discharge of human waste and controlling the discharge of animal waste, this TMDL will also protect the beneficial uses of the Napa River watershed’s aquatic ecosystem, such as cold and warm freshwater habitat, and wildlife habitat.

7.8.2.1    Problem Statement

Due to the presence of pathogens in the Napa River and its tributaries, the beneficial uses of water contact and noncontact recreation are impaired. Waterborne pathogens pose a risk to human health. In ambient waters, the presence of human and animal fecal waste and associated pathogens is inferred from high concentrations of fecal coliform and E. coli bacteria. Bacteria levels in the Napa River and its tributaries are higher than the bacteria water quality objectives established to protect people who swim, wade and fish in these waters (Table 3-1). Consequently, humans who recreate in the Napa River and its tributaries are at risk of contracting waterborne disease.

7.8.2.2    Sources

The following source categories have the potential to discharge pathogens to surface waters in the Napa River watershed:

• On-site sewage disposal systems (septic systems)
  
• Sanitary sewer systems
  
• Municipal runoff
  
• Grazing lands
  
• Confined animal facilities
  
• Municipal wastewater treatment facilities
  
• Wildlife
  

Water quality monitoring data indicate that on-site sewage disposal systems are potentially a significant pathogen source, primarily in the Murphy Creek, Browns Valley Creek, and Salvador Channel subwatersheds. Sanitary sewer lines are a likely source, primarily in the Browns Valley Creek and Salvador Channel sub watersheds. Municipal runoff is a significant source in all urban areas, and livestock grazing and confined animal facilities are considered to be potential sources throughout the watershed.

Both discharger monitoring reports and in-stream water quality monitoring indicate that municipal wastewater treatment facility discharges are not significant pathogen sources in the Napa River watershed. These facilities are considered potential sources due to the possibility of spills or treatment system malfunction.

Wildlife are not a significant, widespread pathogen source, as evidenced by low indicator bacteria levels at sites that contain wildlife but are minimally impacted by human activities. Wildlife may be a significant source on a limited, localized basis.

7.8.2.3    Numeric Targets

The numeric water quality targets listed in Table 7.8.2-1 are derived from water quality objectives for coliform bacteria in contact recreational waters, and from U.S. EPA’s bacteriological criteria (Tables 3-1 and 3-2). The last target, “zero discharge of untreated or inadequately treated human waste,” is consistent with Discharge Prohibition 15 (Table 4-1). The zero human waste discharge target is necessary because human waste is a significant source of pathogenic organisms including viruses; and attainment of fecal coliform targets alone may not be sufficient to protect human health. These bacteria targets, in combination with the human waste discharge prohibitions, are the basis for the TMDL and load allocations, and fully protect beneficial uses.

7.8.2.4    Total Maximum Daily Load

The TMDL, as indicated in Table 7.8.2-2, is expressed as density-based total coliform, fecal coliform, and E. coli bacteria limits.

7.8.2.4    Load Allocations

Density-based pollutant allocations for pathogen source categories (except wastewater treatment facilities) are shown in Table 7.8.2-3. Table 7.8.2-4 presents wasteload allocations for individual municipal wastewater dischargers. Due to the inherent uncertainty in estimating pathogen loading from nonpoint sources and municipal runoff (Table 7.8.2-3), allocations for these source categories incorporate a 10 percent margin of safety. Each entity in the watershed is responsible for meeting its source category allocation.

All discharges of raw or inadequately treated human waste are prohibited. All sources of untreated or inadequately treated human waste have an allocation of zero.

Discharging entities will not be held responsible for uncontrollable discharges originating from wildlife. If wildlife contributions are found to be the cause of exceedances, the TMDL targets and allocation scheme will be revisited as part of the adaptive implementation program.

7.8.2.5    Implementation Plan

This plan builds upon previous and ongoing successful efforts to reduce pathogen loads in the Napa River and its tributaries, and requires actions consistent with the California Water Code (CWC Section 13000 et seq.); the state’s Nonpoint Source Pollution Control Program Plan (CWC Section 13369) and its Policy for Implementation and Enforcement of the Nonpoint Source Pollution Control Program; and the human waste discharge prohibition.

Table 7.8.2-5 contains the required implementation measures for each of the source categories listed in Table 7.8.2-3 and 7.8.2-4. These measures include evaluation of operating practices; development of comprehensive, site-specific pathogen control measures and a corresponding implementation schedule; and submittal of progress reports documenting actions undertaken. Progress reports may be submitted directly to the Water Board or to third parties if designated. These reports will serve as documentation that source reduction measures are being implemented.

It is important to note that the numeric targets and load allocations in the TMDL are not directly enforceable. To demonstrate attainment of applicable allocations, responsible parties must demonstrate that they are in compliance with specified implementation measures and any applicable waste discharge requirements (WDRs) or waiver conditions.

The state’s Policy for Implementation and Enforcement of the Nonpoint Source Pollution Control Program requires that current and proposed nonpoint source discharges be regulated under WDRs, waivers of WDRs, Basin Plan prohibitions, or some combination of these tools. Table 7.8.2-6 specifies the regulatory framework for each discharger source category. The Water Board intends to work with stakeholders to develop conditions for waiving WDRs for grazing lands by 2009.

Cost estimate: Agricultural Water Quality Control Program

Because the implementation measures for grazing lands constitute an agricultural water quality control program, the cost of that program is estimated below, consistent with California Water Code requirements (Section 13141).

The average annual program implementation cost to agricultural dischargers is estimated to range between $60,000 and $250,000 for the next 10 years. These costs will be shared by Napa River watershed grazing lands operators (approximately 20). This estimate includes the cost of implementing animal waste controls and grazing management measures, and is based on costs associated with technical assistance and evaluation, installation of water troughs, and livestock control fencing along up to 25 percent of streams in grazing lands. Besides fencing, other acceptable methods of managing livestock access to streams are not included in this cost estimate due to variability in costs and site-specific applicability. In addition to private funding, potential sources of financing include federal and state water quality grants and federal agricultural grants.

Evaluation and Monitoring

Beginning in 2011 and approximately every five years thereafter, the Water Board will evaluate site-specific, subwatershed-specific, and watershed-wide compliance with the trackable implementation measures specified in Table 7.8.2-5. In evaluating compliance with the trackable implementation measures, the Water Board will consider levels of participation for each source category as well as for individual dischargers (as documented by Water Board staff or third parties).

In addition to the programmatic monitoring described above, Water Board staff, in collaboration with stakeholders, will conduct water quality monitoring to evaluate E. coli concentration trends in the Napa River and its tributaries. Five years after TMDL adoption, the Water Board will evaluate monitoring results and assess progress made toward attaining TMDL targets (Table 7.8.2-1) and load allocations (Table 7.8.2-3). The main objectives of the Monitoring Program are to:

• Assess attainment of TMDL targets
  
• Evaluate spatial and temporal water quality trends
  
• Further identify significant pathogens source areas
  
• Collect sufficient data to prioritize implementation efforts and assess the effectiveness of source control actions
  
• Collect sufficient data to evaluate the costs of pathogen source control measures and the existence of other pollutant reduction benefits (e.g., nutrients or sediment), if any

Table 7.8.2-7 presents locations for baseline water quality monitoring. Each site will be sampled for E. coli ten times each year. Five samples will be collected weekly during one 30-day period in each wet season (November through March) and one 30-day period in each dry season (May through September). All water quality monitoring (including quality assurance and quality control procedures) will be performed pursuant to the State Water Board’s Quality Assurance Management Plan for the Surface Water Ambient Monitoring Program. Additional monitoring will be conducted as needed if funds are available. In lieu of the monitoring plan described in Table 7.8.2-7, one or more implementing parties may submit an alternative monitoring plan for Executive Officer approval.

If source control actions are fully implemented throughout the watershed and the TMDL targets are not met, the Water Board may consider whether the TMDL targets are attainable, and re-evaluate or revise the TMDL and allocations as appropriate. Alternatively, if the required actions are not implemented or are only partially implemented, the Water Board may consider regulatory or enforcement action against dischargers not in compliance.

Adaptive Implementation

Approximately every five years, the Water Board will review the Napa River Pathogen TMDL and evaluate new and relevant information from monitoring, special studies, and the scientific literature. At a minimum, the following questions will be included in the reviews. Additional questions will be developed in collaboration with stakeholders during each review cycle.

• Are the river and the tributaries progressing toward TMDL targets as expected? If progress is unclear, how should monitoring efforts be modified to detect trends? If there has not been adequate progress, how might the implementation actions or allocations be modified?
• What are the pollutant loads for the various source categories (including naturally occurring background pathogen contributions and the contribution from open space lands)? How have these loads changed over time, how do they vary seasonally, and how might source control measures be modified to improve load reduction?
• Is there new, reliable, and generally accepted scientific information that suggests modifications to targets, allocations, or implementation actions? If so, how should the TMDL be modified?

Reviews will be coordinated by the Water Board’s continuing planning program, with stakeholder participation. Any necessary modifications to the targets, allocations, or implementation plan will be incorporated into the Basin Plan via an amendment process. In evaluating necessary modifications, the Water Board will favor actions that reduce sediment and nutrient loads, pollutants for which the Napa River watershed is also impaired.

7.8.3 Sonoma Creek Watershed Sediment TMDL and Habitat Enhancement Plan

The goals of the Sonoma Creek Watershed Sediment TMDL and Habitat Enhancement Plan (Plan) are to:

• Conserve the steelhead trout population
• Restore water quality to meet water quality standards, including attaining beneficial uses
• Enhance the overall health of the native fish community
• Protect and enhance habitat for native aquatic species
• Enhance the aesthetic and recreational values of the creek and its tributaries

To achieve these goals, specific actions are needed to:

1. Reduce sediment loads, and fine sediment in particular, to Sonoma Creek and its tributaries
2. Attain and maintain suitable gravel quality in freshwater reaches of Sonoma Creek and its tributaries
3. Reduce and prevent channel incision
4. Reduce erosion and sedimentation
5. Repair large sources of sediment supply (e.g., landslides)
6. Enhance channel complexity (e.g., by adding and encouraging retention of large woody debris and restoring riparian vegetation)

The following sections establish:

1. A sediment total maximum daily load (TMDL) defining the allowable amount of sediment that can be discharged into Sonoma Creek, expressed as mass, and as a percentage of the natural background sediment delivery rate to channels
2. An implementation plan to achieve the TMDL and related habitat enhancement goals

7.8.3.1         Problem Statement

Steelhead populations in the Sonoma Creek watershed have declined substantially since the late 1940s. Results of recent analyses of fisheries and sediment sources indicate that:

1. Excessive amounts of fine sediment have been deposited in the streambed at potential steelhead spawning and rearing sites. Excess fine sediment in the streambed can cause poor incubation conditions for fish eggs, resulting in high mortality prior to emergence. Fine sediment also compromises the quality of pools as rearing habitat, and reduces winter rearing habitat by filling the spaces between cobbles and boulders.
2. Changes in physical habitat structure that appear to be caused by erosion of bed and banks (incision) in Sonoma Creek are resulting in significant adverse changes to steelhead habitat. Analysis of in-stream shelter in Sonoma Creek yielded a low score when considering the watershed-wide average (38, which is 13 percent of the maximum score), indicating low quality of rearing habitat for juvenile steelhead. A steelhead census performed in 2002 indicates only 10 percent of steelhead are surviving past the juvenile rearing stage. These conditions are limiting the success of steelhead fish in Sonoma Creek.
3. Stressful water temperatures, low summer flows, and migration barriers also impact the health of Sonoma Creek’s coldwater fishery.

Due to excess erosion and sedimentation in the Sonoma Creek Watershed, the narrative water quality objectives for sediment and settleable material are not being met and cold freshwater habitat, wildlife habitat, fish spawning, recreation, and preservation of rare and endangered species beneficial uses are impaired. In addition, channel incision has caused habitat simplification, which has reduced and quantity and quality of spawning and rearing habitat for salmonids and other native aquatic species. Channel incision is a controllable water quality factor that is contributing to a violation of the narrative water quality objective for population and community ecology.

7.8.3.2         Numeric Targets and Desired Condition

Meeting the numeric targets and desired condition listed in Table 7.8.3-1 will allow water quality in Sonoma Creek and its tributaries to achieve the Basin Plan’s narrative water quality objectives for sediment, settleable material, and population and community ecology.

7.8.3.3         Sources

Field assessments and sediment load modeling provide credible estimates of average rates of sediment delivery to Sonoma Creek. As shown in Table 7.8.3-2, the average annual sediment load to the freshwater reach of Sonoma Creek is estimated to be 117,000 tons per year, or 360 tons per km2  per year. The natural background sediment delivery rate to Sonoma Creek is 52,000 tons per year, or 160 tons per km2  per year. Therefore, the current sediment delivery rate is estimated to be 225 percent of the natural background rate.

7.8.3.4         Total Maximum Daily Load and Allocations

The Sonoma Creek sediment TMDL is established at 65,400 tons per year, which is approximately 125 percent of natural background load. Natural background load depends upon natural processes, and varies significantly.  Therefore, the TMDL and allocations are expressed both in terms of sediment mass and percent of natural background. The percentage based TMDL, 125% of natural background, applies throughout the watershed. In order to achieve the TMDL, controllable sediment delivery resulting from human actions needs to be reduced by approximately 80 percent from current proportion of the total load (Table 7.8.3-3). TMDL attainment will be evaluated at the limit of tidal influence in the Sonoma Creek watershed, which approximates the downstream boundary of freshwater habitat for steelhead.  Sonoma Creek has several tributaries that join the mainstem below the tidal limit; therefore, several points will be used to evaluate TMDL attainment. These points are: mainstem Sonoma Creek just downstream of the Fowler/Carriger Creek confluence, and the freshwater portions (above tidal influence) of Schell, Ramos, Carneros, and Merazo Creeks. Attainment of the TMDL will be evaluated over a 5-to-10-year averaging period. The TMDL equal to 125 percent of natural background load, can be achieved if human-related sources are reduced to the level of the allocations shown in Table 7.8.3-3.

7.8.3.5         Implementation Plan

The implementation actions described below are to achieve TMDL targets and allocations and habitat enhancement goals. In addition, actions specified in this plan are expected to enhance steelhead population. It is important to note that the allocations in the TMDL are not directly enforceable. To demonstrate attainment of applicable allocations, responsible parties must demonstrate that they are in compliance with required implementation measures and any applicable waste discharge requirements (WDRs), WDR waiver conditions, or NPDES permits.

Regulatory Tools

The State’s Policy for Implementation and Enforcement of the Nonpoint Source Pollution Control Program requires regulation of nonpoint source discharges using the Water Board’s administrative permitting authorities, including WDRs, waivers of WDRs, Basin Plan Discharge Prohibitions, or some combination of these. Consistent with this policy, Tables 7.8.3-4 – 7.8.3-7 (Table 7.8.3-4, Table 7.8.3-5, Table 7.8.3-6, Table 7.8.3-7) specify actions and performance standards by nonpoint source category, as needed to achieve TMDL sediment targets and allocations in the Sonoma Creek watershed. The Water Board will consider adopting conditions for waiving WDRs that apply to the nonpoint sources (vineyards, grazing, roads, etc.) listed in Tables 7.8.3-4 – 7.8.3-7 (Table 7.8.3-4, Table 7.8.3-5, Table 7.8.3-6, Table 7.8.3-7), address all pollutants of concern, protect all beneficial uses, and balance the agricultural, environmental, recreational, and residential needs of the watershed.

The wasteload allocations contained in Table 7.8.3-3 apply to point sources of sediment that are regulated by NPDES permits. Table 7.8.3-8 shows implementation measures required of these sources, which include municipal stormwater, runoff from state highways, and from industrial and construction sites.

Problems associated with channel incision, related rapid bank erosion, and loss of essential habitat features, reflect and integrate multiple historical and ongoing disturbances, some of which are local and direct, and others that are indirect and distal. Effectively addressing these issues will require cooperative and coordinated actions by multiple landowners, working with public agencies, over significant distances along the creek. The most effective means of controlling channel incision and reducing related fine sediment delivery to the creek is a channel restoration program that re-establishes width-to-depth ratios and sinuosity values conducive to formation of alternate bars and a modest flood plain. The Water Board will work with stakeholders along Sonoma Creek, through local stewardship groups, to implement such channel restoration/habitat enhancement projects. Table 7.8.3-9, Table 7.8.3-10, and 7.8.3-11 (Recommended Measures to Protect or Enhance Habitat), specify actions to address adverse impacts of channel incision on salmonid habitat quantity and quality, and to accomplish habitat enhancement goals for flow, temperature, and fish passage for steelhead. 

Individual landowners or coalitions may work with “third parties” to develop and implement sediment pollutant control programs. With regard to achievement of actions to protect or enhance baseflow, fish passage, habitat complexity, and stream temperature, the effectiveness of the recommended actions specified in Tables 7.8.3-9, 7.8.3-10 and 7.8.3-11, will be evaluated as part of the adaptive implementation program.

Agricultural Water Quality Control Program Costs

Implementation measures for grazing lands and vineyards constitute an agricultural water quality control program and therefore, consistent with California Water Code requirements (Section 13141), the cost of this program is estimated herein.  This cost estimate includes the cost of implementing all actions to reduce sediment discharges and enhance habitat complexity as specified in the implementation plan, and is based on costs associated with technical assistance and evaluation, project design, and implementation of actions needed to achieve the TMDL. In estimating costs, the Water Board has assumed that owners of agricultural businesses own 75 percent of total land area on hillside parcels, and 95 percent of the land along Sonoma Creek and lower reaches of its tributaries. Based on these assumptions, the estimated total cost for program implementation for agricultural sources is $1.3-to-2.3 million per year throughout the 20-year implementation period. More than three-quarters of these potential costs are associated with addressing channel incision and enhancing habitat conditions (to reverse the impacts of channel incision) in Sonoma Creek and its tributaries. Considering potential benefits to the public in terms of ecosystem functions, aesthetics, recreation, and water quality, it is anticipated that at least 75 percent of the cost of these actions will be paid for with public funds. Therefore, the total cost to agricultural businesses associated with efforts to reduce sediment supply and enhance habitat in Sonoma Creek is $300,000-$600,000 per year over the 20-year implementation period.

Evaluation and Monitoring

In collaboration with stakeholders in the watershed, Water Board staff will develop a detailed monitoring program to assess progress of TMDL attainment and provide a basis for reviewing and revising TMDL elements or implementation actions. As an initial milestone, by fall 2011, the Water Board and watershed partners will complete monitoring plans to evaluate: a) attainment of water quality targets; and b) suspended sediment and turbidity conditions. Initial data collection, based on the protocols established in these monitoring plans is anticipated to begin in the winter of 2011-2012.

As a whole, the monitoring program will be designed to:

1. Assess channel response and progress towards achieving water quality targets. In-channel effectiveness monitoring will be conducted to evaluate: a) progress toward achieving water quality targets, and b) channel response to management measures and natural processes. Parameters that will be monitored to assess progress toward achieving water quality targets are streambed permeability, pool filling, and percent fines composition of the substrate. The number of sites to be monitored will be selected based on availability/presence of the applicable habitat feature (i.e., spawning gravels and pools), as well as the number of samples needed to have a high degree of statistical confidence in estimated values. Frequency of monitoring should be once every five years, at a minimum, for streambed permeability and pool filling. If resources are available, desired monitoring frequency for all TMDL target parameters is once every two to three years. Pool filling should be monitored every two to three years to allow a trend analysis. The Water Board may establish alternative water quality parameters and/or numeric target values at a future date as part of the adaptive implementation process, when/if information becomes available to conclude with a high degree of confidence that one or more alternative parameters or target values provide a superior basis for determining attainment of water quality objectives for sediment, and the protection of fisheries-related beneficial uses.


2. Further evaluate potential impacts of suspended sediment and related turbidity.  To further study potential impacts of suspended sediment and related turbidity, monitoring of turbidity should continue. The Sonoma Ecology Center maintains a continuous and automated monitoring station at the Sonoma Valley Watershed Station in Eldridge, CA. Monitoring of suspended sediment should continue to further understanding of turbidity and suspended sediment concentrations in ambient conditions, and during and after storms. Turbidity/suspended sediment data should be analyzed to determine the length of time it takes for turbidity levels to drop to pre-storm levels after a storm event.

   It is expected that as sediment reduction and habitat enhancement measures (including reducing channel incision) are undertaken, suspended sediment concentrations and turbidity levels will decrease. This expectation should be confirmed with continued turbidity monitoring. In addition, turbidity monitoring can provide information regarding the effectiveness of sediment reduction measures because it is a sensitive measure of the effects of land use on streams.

3. Assess whether required sediment reduction measures are undertaken. Implementation monitoring will be conducted by landowners or designated agents, per the compliance monitoring and reporting provisions of applicable waivers of WDRs, WDRs, and NPDES permits.


4. Evaluate effectiveness of selected sediment reduction measures (both structural and management-related). The Water Board will conduct upslope effectiveness monitoring to evaluate sediment delivery to channels from land use activities and natural processes. The first sediment source analysis update will occur by 2020, when sediment delivery associated with human activities may be reduced by 25 percent or more. A subsequent update may occur, assuming the water quality targets for sediment are not already achieved, by 2025, when sediment supply associated with human activities may be reduced by 40 percent or more. An additional goal for future updates of the source analysis is to reduce uncertainty associated with estimates of sediment delivery rates.


5. Evaluate effectiveness of recommended habitat enhancement measures and assess progress towards goals of the Habitat Enhancement Plan. The Water Board and local partners should monitor habitat complexity-related water quality indicators to assess progress towards achievement of a balanced sediment budget (where the amount of fine and course sediment input to a given channel reach is equal to the amount that is transported downstream).

   Monitoring should occur to determine whether there is an increasing trend in the percent of the length of mainstem of Sonoma Creek, and in the lower alluvial reaches of its tributaries, that attain the following conditions:

   1. The bankfull channel width-to depth ratio is > 12:1.
   2. The average spacing between alluvial and/or forced gravel bars within the active channel is <  7 times the width of the bankfull channel.
   3. Available shear stress at bankfull flow does not exceed the amount required to initiate motion of the streambed by more than approximately 20 percent.
   4. Floodplain width is > 4 times bankfull channel width.
   
   

   Monitoring should also assess whether there is:

   5. An increasing trend through time in the mean area and frequency of riffles and gravel bars within the mainstem channel; and
   6. A decreasing trend through time in the percent of the length of the mainstem of Sonoma Creek, and in the lower alluvial reach of its tributaries, where banks or bed are hardened, and/or where constructed levees contribute to channel instability.
   
   

   The information gained from monitoring will guide adaptive implementation.

7.8.3.6         Adaptive Implementation

In concert with the monitoring program, described above, the Sonoma Creek Watershed Sediment TMDL and Habitat Enhancement Plan will be regularly updated. Results of in-progress or anticipated studies that enhance understanding of the population status of steelhead trout in the Sonoma Creek watershed, and/or factors controlling those populations, may also trigger changes to the plan and TMDL. At a minimum, data in response to the following questions will be considered to guide research and monitoring efforts and focus each subsequent update of the TMDL.

Key Questions to be considered in the course of Adaptive Implementation:

• What is the population status of steelhead in the watershed? Is there an increase in the number or percentage of steelhead that survive past the juvenile rearing life stage as sediment reduction and habitat enhancement measures are implemented?  An improved understanding of the current status of steelhead populations in the Sonoma Creek watershed is essential for guiding adaptive updates to the management actions recognized in this plan. Two types of monitoring data may be needed to evaluate the current population status in the watershed: 1) “smolt” production and sizes, and 2) adult spawning run-size. Smolt refers to the life stage when juvenile salmonids migrate from freshwater to the ocean. These two types of monitoring would provide a basis for assessing the influences of ocean and freshwater rearing habitat on steelhead run-size.
• Are Sonoma Creek and its tributaries progressing toward TMDL targets as expected? If there has not been adequate progress, how might the implementation actions, targets or allocations be modified?
• What are expected benefits of various actions to enhance habitat for steelhead? Which actions, and in which locations, would enhancement measures have the most benefit and be the most cost-effective?
• Are the specified sediment reduction measures and recommended habitat enhancement measures resulting in an improving trend in channel stability?
• What effect will climate change have on hydrology, sediment transport, and habitat for the watershed’s aquatic species? Is there evidence that TMDL implementation actions, together with climate change, may affect Bay tidal habitats? How will climate change effect the outcome of required and recommended measures, and how should these measured be adjusted in response?
• Are there new data or information available that warrants revision of water quality targets, allocations, or implementation measures?

7.8 4 Napa River Sediment Reduction and Habitat Enhancement Plan

The goals of the Napa River Sediment Reduction and Habitat Enhancement Plan (Plan) are to:

• Conserve the steelhead trout population
• Establish a self-sustaining Chinook salmon population
• Enhance the overall health of the native fish community
• Enhance the aesthetic and recreational values of the river and its tributaries

To achieve these goals, specific actions are needed to:

• Attain and maintain suitable gravel quality and diverse streambed topography in freshwater reaches of Napa River and its tributaries
• Protect and/or enhance base flows in tributaries and the mainstem of the Napa River
• Reduce the number and significance of human-made structures in channels that block or impede fish passage
• Maintain and/or decrease summer water temperatures in tributaries to the Napa River

The following sections establish:

1. A sediment total maximum daily load (TMDL) defining the allowable amount of sediment that can be discharged into the Napa River, expressed as a percentage of the natural background sediment delivery rate to channels
2. An implementation plan to achieve the TMDL and related habitat enhancement goals

7.8.4.1         Problem Statement

Steelhead and salmon populations in the Napa River and its tributaries have declined substantially since the late 1940s. Results of recent analyses of fisheries and sediment sources indicate that:

1. Spawning and juvenile rearing habitat for salmon and steelhead are adversely affected by high concentrations of fine sediment (primarily sand) deposited in the bed of the Napa River and its tributaries.

Successful reproduction by salmon and steelhead depends on adequate flow through streambed gravels (permeability) in order for eggs to hatch and larvae to grow. As the concentration of fine sediment (primarily sand) in the streambed increases, permeability decreases, which in turn increases egg and larval mortality, and ultimately causes a decrease in the number of young fish that emerge from the streambed. Similarly, as the concentration of sand in the streambed increases, the frequency and extent of streambed scour is intensified, further increasing mortality between spawning and emergence by washing eggs and/or larvae out of the bed during common high flow events.

Even small increases in the concentration of fine sediment in the streambed may degrade the quality of rearing habitat for juvenile steelhead and salmon. Young steelhead need open spaces between clusters of large cobbles and boulders in order to escape high flows and predation during the winter. Similarly, as the concentration of fine sediment in the streambed increases, growth and survival of juvenile steelhead and salmon decreases as a consequence of lower biomass of aquatic insect prey species, and increasing activity level, aggressive behavior, and attacks between juvenile salmon and steelhead as they compete for food. 

2.  Channel incision has greatly reduced the quantity and quality of spawning and rearing habitat for Chinook salmon in Napa River watershed. Habitat losses as a result of incision exert a significant negative influence on freshwater growth and survival of juvenile salmon, and therefore, on the number of Chinook salmon that ultimately return to spawn. 

Channel incision, the progressive lowering over time of streambed elevation as a result of net erosion, has lowered the streambed of the mainstem of the Napa River by more than two meters since the start of the current episode of incision, which began sometime after 1965. As a result, habitat is being degraded. The channel has become isolated from its flood plain and there has been a large reduction in the size and frequency of riffles, gravel bars, side channels, and sloughs. These habitats provide essential spawning and juvenile rearing habitat for Chinook salmon. Human activities that have contributed to channel incision in the River, including (but not necessarily limited to) levee building, development projects that have increased peak runoff during storms, construction of large tributary dams, straightening of some mainstem channel reaches, filling of side channels, historical gravel mining, dredging to reduce flood risk, and intensive removal of large woody debris. 

3. Low flows and stressful water temperatures during the spring and dry season, and fish migration barriers exert a significant negative influence on the number (and fitness) of juvenile steelhead that migrate to the ocean from the watershed, and as such, on the number of adults that successfully return to spawn. 

Drifting aquatic insects produced in riffles often are the primary source of food for juvenile steelhead. Low or no flow over riffles during the spring and dry season greatly reduces this food source. An association between low and/or negative growth rates in juvenile steelhead and poor baseflow persistence was documented in the summer and fall of 2001 in Napa River watershed. Summer water temperatures in tributaries also are often stressful to juvenile steelhead, likely contributing to poor growth rates that were documented. If low growth rates in summer are not mitigated by high rates of growth during other times of the year, significant reductions in survival rates during all subsequent life stages may result.

Poor access to and from potential spawning and rearing habitat due to man-made structures built in channels (e.g., dams, road crossings, weirs, etc.) and human water uses have reduced the size of the steelhead run in the Napa River watershed. For example, approximately 30 percent of the land area in the Napa River watershed drains into over 400 on-channel reservoirs. 

Due to excess erosion and sedimentation in the Napa River watershed, the narrative water quality objectives for sediment and settleable material are not being met, and cold freshwater habitat, wildlife habitat, fish spawning, recreation, and preservation of rare and endangered species beneficial uses are impaired. In addition, channel incision has reduced the quantity of gravel bars, riffles, side channels, and sloughs, which threatens Chinook salmon and other fish and aquatic wildlife species. Channel incision is a controllable water quality factor that is contributing to a violation of the narrative water quality objective for population and community ecology.

7.8.4.2         Numeric Targets

Meeting the numeric targets listed in Table 7.8.4-1 will allow water quality in the Napa River and its tributaries to achieve the Basin Plan’s narrative water quality objectives for sediment, settleable material, and population and community ecology.

 

7.8.4.3         Sources

Field inventories conducted throughout the watershed provide credible estimates of the rates and sizes of sediment delivered to Napa River watershed channels between 1994 and 2004. Based on this work, and application of channel and reservoir mapping, the Water Board concludes that:

1. More than half of fine sediment delivered to Napa River during the 1994–2004 period is associated with land use activities, including roads, human-caused channel incision, vineyards, intensive historical livestock grazing, and urban stormwater runoff. 
   
2. In addition to its prominence in the sediment budget, channel incision is the primary agent for isolation of the channel from its flood plain and a reduction in the quantity and frequency of spawning and rearing habitat for salmon and steelhead in Napa River and the lower reaches of its tributaries.
   
3. Channel sediment loads vary greatly depending upon nature of underlying bedrock or sediment deposits, land use activities, and the location of dams.
   
4. Thirty percent of the watershed drains into reservoirs constructed in tributary channels. These reservoirs capture all of the gravel and sand, and most of the finer sediment input to upstream channels. Nonetheless, anthropogenic activities, downstream of dams, are contributing enough sediment such that the fine sediment load is substantially elevated in the Napa River downstream of the reservoirs.

Mean annual sediment delivery rate to channels is estimated to have been  272,000 metric tons per year during the period from 1994 to 2004, which when considered in relation to the land area draining into the Napa River at Soda Creek (e.g., 584 km2), equals  466 metric tons per km2 per year (Table 7.8.4-2). The natural background rate of sediment delivery during this period, absent dams and human-caused erosion is estimated to have been 252 metric tons per km2 per year, which is calculated from Table 7.8.4-2 as follows:

48,000 metric tons/year–sediment deposited in tributary reservoirs
7,000 metric tons/year–sediment discharged through dams on tributaries
92,000 metric tons/year–input to channels downstream of reservoirs
147,000 metric tons/year

147,000 metric tons/584 km²–land area draining to Napa R. at Soda Creek
                                              =252 metric tons/km²/year

Therefore total sediment load in the Napa River at Soda Creek is estimated to have been 185 percent of natural background (e.g., 466/252 = 185%) during 1994-2004. Table 7.8.4-2 breaks down the sediment sources to the Napa River, with annual average rate calculated at Soda Creek over the 10-year study period.

7.8.4.4         Total Maximum Daily Load and Allocations

The Napa River sediment TMDL is established at 185,000 metric tons per year, which is approximately 125 percent of natural background load (based on sediment load estimates from the 1994-2004 period) calculated at Soda Creek. Natural background load depends upon natural processes, and varies significantly.  Therefore, the TMDL and allocations are expressed both in terms of sediment mass and percent of natural background. The percentage based TMDL, 125% of natural background, applies throughout the watershed. In order to achieve the TMDL, controllable sediment delivery resulting from human actions needs to be reduced by approximately 50 percent from current proportion of the total load (Tables 7.8.4-3a and 7.8.4-3b). TMDL attainment will be evaluated at the confluence of Napa River with Soda Creek, which approximates the downstream boundary of freshwater habitat for salmon and steelhead.  Attainment of the TMDL will be evaluated over a 5-to-10-year averaging period.

Because dams trap almost all upstream sediment inputs to channels, natural sediment input to channels downstream of dams equals only 62 percent of the total natural background load (e.g., amount that would have been input to Napa River absent dams and human caused erosion). Almost 50 percent of the TMDL can be allocated to human-caused sources. The TMDL equal to 125 percent of natural background load, can be achieved if human-related sources are reduced to the level of the allocations shown in Tables 7.8.4-3a and 7.8.4-3b).

7.8.4.5         Implementation Plan

The actions described below, including the processes by which sediment and runoff control practices are proposed and implemented, are necessary to achieve TMDL targets and allocations and habitat enhancement goals. In addition, actions specified in this plan are expected to enhance steelhead run size and facilitate establishment of a self-sustaining Chinook salmon run.

Regulatory Tools

The only point sources of sediment identified in Tables 7.8.4-2 and 7.8.4-3b are those associated with urban stormwater runoff (e.g., municipal stormwater, runoff from State highways, and industrial and construction discharges) and wastewater treatment plants, which are regulated by NPDES permits. Table 7.8.4-4 shows implementation measures required of these sources.

The state’s Policy for Implementation and Enforcement of the Nonpoint Source Pollution Control Program requires regulation of nonpoint source discharges using the Water Board’s administrative permitting authorities, including waste discharge requirements (WDRs), waiver of WDRs, Basin Plan Discharge Prohibitions, or some combination of these. Consistent with this policy, Tables 7.8.4-4a, 7.8.4-4b, 7.8.4-4c, and 7.8.4-4d specify actions and performance standards by nonpoint source category, as needed to achieve TMDL sediment targets and allocations in Napa River watershed. The Water Board will consider adopting conditions for waiving WDRs that apply to the nonpoint sources (vineyards, grazing, roads, etc.) listed in Tables 7.8.4-4a, 7.8.4-4b, 7.8.4-4c, and 7.8.4-4d, address all pollutants of concern, protect all beneficial uses, and balance the agricultural, environmental, recreational, and residential needs of the watershed.

Problems associated with channel incision, related rapid bank erosion, and loss of essential habitat features, reflect and integrate multiple historical and ongoing disturbances, some of which are local and direct, and others that are indirect and distal. Effectively addressing these issues will require cooperative and coordinated actions by multiple landowners, working with public agencies, over significant distances along the river. The most effective means of controlling channel incision and reducing related fine sediment delivery to the river is a channel restoration program that re-establishes width-to-depth ratios and sinuosity values conducive to formation of alternate bars and a modest flood plain. The Water Board will work with stakeholders along the Napa River, through local stewardship groups, to implement such channel restoration/habitat enhancement projects. Tables 7.8.4-5a, 7.8.4-5b, 7.8.4-5c, and 7.8.4-5d (Recommended Measures to Protect or Enhance Habitat), specify actions to address adverse impacts of channel incision on salmon habitat quantity and quality, and to accomplish habitat enhancement goals for flow, temperature, and fish passage for steelhead and salmon. 

Individual landowners or coalitions may work with “third parties” to develop and implement sediment pollutant control programs. With regard to achievement of actions to protect or enhance baseflow, fish passage, habitat complexity, and stream temperature, the effectiveness of the recommended actions specified in Tables 7.8.4-5a, 7.8.4-5b, 7.8.4-5c, and 7.8.4-5d, will be evaluated as part of the adaptive implementation program.

Minimization of Potential Impacts to Sensitive Natural Communities

In order to minimize potential impacts to sensitive natural communities that may not be fully protected through County regulations, Basin Plan amendment compliance actions will not be required or approved beyond the development footprint authorized by local land-use authorities in any of the following sensitive natural communities within the Napa River watershed:

• Redwood forest
  
• Ponderosa Pine alliance
  
• Tanbark Oak alliance
  
• Oregon white oak woodland
  
• Mixed serpentine chaparral
  
• Wet meadow grasses NFD super alliance.

Locations for these sensitive natural communities and/or land-cover types in the Napa River watershed can be determined by review of the Vegetation Map of Napa County, California (Thorne et al., 2004; http://cain.ice.ucdavis.edu/regional/napavegmap/), the Baseline Data Report (Chapter 4, Jones & Stokes, 2005) and/or the California Natural Diversity Database.

Agricultural Water Quality Control Program Costs

Implementation measures for grazing lands and vineyards constitute an agricultural water quality control program and therefore, consistent with California Water Code requirements (Section 13141), the cost of this program is estimated herein. This cost estimate includes the cost of implementing all actions to reduce sediment discharges and enhance habitat complexity as specified in the implementation plan, and is based on costs associated with technical assistance and evaluation, project design, and implementation of actions needed to achieve the TMDL. In estimating costs, the Water Board has assumed that owners of agricultural businesses (e.g., grape growers and ranchers), within the unincorporated area, own 75 percent of total land area on hillside parcels, and 95 percent of the land along Napa River and lower reaches of its tributaries.  Based on these assumptions, we estimate total cost for program implementation for agricultural sources could be $1.9-to-3.4 million per year throughout the 20-year implementation period.  More than two-thirds of these potential costs are associated with reducing sediment discharges and enhancing habitat conditions (to address channel incision) in Napa River. Considering potential benefits to the public in terms of ecosystem functions, aesthetics, recreation, and water quality, it is anticipated that at least 75 percent of the cost of these actions will be paid for with public funds. Therefore, the total cost to agricultural businesses associated with efforts to reduce sediment supply and enhance habitat in Napa River is $800,000 to $1.7 million per year. 

7.8.4.6         Evaluation and Monitoring

Three types of monitoring are specified to assess progress toward achievement of numeric targets and load allocations for sediment:

1. Implementation monitoring to document that required sediment control and habitat enhancement actions are implemented
   
2. Upslope effectiveness monitoring to evaluate effectiveness of sediment control actions in reducing rates of sediment delivery to channels
3. In-channel effectiveness monitoring (e.g., spawning gravel permeability and redd scour) to evaluate channel response to management actions and natural processes

Implementation monitoring will be conducted by landowners or designated agents. The purpose of this type of monitoring is to document that sediment control and/or habitat enhancement actions specified herein actually occur.  

The Water Board will conduct upslope effectiveness monitoring to evaluate sediment delivery to channels from land use activities and natural processes. The first update will occur on or before the fall of 2017, when sediment delivery associated with land use activities should be reduced by 25 percent or more. A subsequent update may occur, assuming the numeric targets for sediment are not already achieved, on or before the fall of 2022, when sediment supply associated with land use activities should be reduced by 37 percent or more.

In-channel effectiveness monitoring should be conducted by local government agencies with scientific expertise and demonstrated capability in working effectively with private property owners (to gain permissions for access), as needed to develop a representative sample of stream habitat conditions, in relation to sediment supply and transport within the watershed. In addition, the Water Board will conduct in-channel effectiveness monitoring as part of the Surface Water Ambient Monitoring Program. In-channel effectiveness monitoring needs to include measurements of redd scour and spawning gravel permeability to evaluate attainment of water quality objectives for sediment, settleable material, and population and community ecology. To establish a high level of statistical confidence in estimated values, spawning gravel permeability will need to be measured at 150 or more potential spawning sites located in ten-or-more tributaries, and 50 or more potential spawning sites in the mainstem of the Napa River.  Redd scour will need to be measured in the mainstem Napa River at approximately 30 or more potential spawning sites, with 4 or more scour measurements per spawning site. Desired frequency for measurement of permeability and redd scour is once every two to three years. At a minimum, repeat surveys will be conducted once every five years.

In addition to the above described monitoring program to evaluate attainment of numeric targets for sediment, the Water Board will monitor turbidity and residual pool volume. Monitoring will be conducted in a subset of the channel reaches where spawning gravel permeability and/or redd scour are measured. Stream temperature and baseflow persistence will be monitored as part of the Surface Water Ambient Monitoring Program.

7.8.4.7         Adaptive Implementation

In concert with the monitoring program, described above, the Napa River Sediment Reduction and Habitat Enhancement Plan and TMDL will be regularly updated. Results of in-progress or anticipated studies that enhance understanding of the population status of steelhead trout and Chinook salmon in Napa River watershed, and/or factors controlling those populations, may also trigger changes to the plan and TMDL. At a minimum, data in response to the following questions will be considered to guide research and monitoring efforts and focus each subsequent update of the TMDL.

Key Questions to be considered in the course of Adaptive Implementation:

1. What is the population status of steelhead and salmon in the watershed? An improved understanding of the status of steelhead and salmon populations in the Napa River watershed is essential for guiding adaptive updates to the management actions recognized in this plan.

Two types of monitoring data may be needed to evaluate the population status of steelhead in the Napa River watershed: 1) “smolt” production and sizes, and 2) adult spawning run-size. Smolt refers to the life stage when juvenile salmon and trout migrate from freshwater to the ocean. Estimates of smolt production and sizes, and inter-annual variation in these parameters, can provide a strong basis for evaluating population status of ocean migrating species of trout and salmon, and influence of freshwater rearing habitat conditions on number of adults that successfully return to spawn. At least five years of monitoring (trapping) of ocean migrating smolts are needed to evaluate current steelhead population status. In addition to smolt trapping, three or more years of monitoring data are needed to estimate the number of adult steelhead returning to spawn. This information, when combined with estimates of smolt production and sizes, would provide a basis for assessing the influences of ocean and freshwater habitat on steelhead run-size, for validating smolt production estimates and predictions regarding ocean survival, and ultimately for evaluating the status of the steelhead population in the watershed.

A similar monitoring program is needed to evaluate the population status of the Chinook salmon in the Napa River watershed. Such a program might include the following elements: 1) adult spawning run-size and genetic structure; 2) smolt production; and 3) egg survival from spawning to emergence (emergence trapping). During the past two years, the Napa County Resource Conservation District has conducted surveys to estimate the number of adult salmon returning to spawn. These surveys should continue for at least three more years, both to estimate the number of spawners and inter-annual variations, and to collect fin clips, as needed to evaluate origins of the spawning adults (e.g., returning adults or strays from hatcheries or other streams). The hypothesis that Chinook salmon experience very high rates of mortality during all freshwater life stages in the Napa River watershed, could be confirmed or rejected through direct monitoring of egg survival to emergence (emergence trapping), fry survival and growth, and smolt trapping.  

2. What are expected benefits of various actions to enhance habitat for steelhead and salmon? For steelhead, the results of in-progress studies of juvenile growth and survival will enhance understanding of the significance of dry season base flow and temperature as potential limiters on steelhead run-size.  Other information needed to refine the understanding of primary constraints on steelhead population size includes the following: a) comprehensive fish passage evaluations in all key tributaries that provide potential habitat for steelhead; b) dry season water-level monitoring in the same tributaries conducted over two-or-more consecutive years; and c) field surveys to evaluate winter rearing habitat quantity and quality. Given the above sources of information, it may be possible to accurately predict relative increases (high, medium, low) in smolt production associated with various management actions (e.g., baseflow enhancement, fish passage enhancement, reduction in fine sediment supply, etc.) in various locations throughout the watershed.

Key information sources needed to refine understanding of primary controls on Chinook salmon population size include egg survival-to-emergence and controls (e.g., redd scour, gravel permeability), fry survival and growth, and number and sizes of juvenile salmon migrating to the ocean. To this end, pre-and-post project monitoring associated with the proposed Rutherford channel enhancement project may provide an opportunity to determine the amount and types of habitat enhancement actions needed to support a self-sustaining run of Chinook salmon, and to enhance the overall health of the native fish community within the watershed. Key parameters that might be monitored to evaluate fisheries’ response to channel enhancement could include: a) changes in quantity, quality, and frequency of key habitat types (e.g., riffles, pools, side channels, gravel bars); b) spawning gravel permeability and scour; c) base flow persistence and temperature; and d) relative abundance of native and introduced fish species. 

7.8.5 Petaluma River Bacteria Total Maximum Daily Load (TMDL)

The following sections establish the TMDL for bacteria in Petaluma River and its tributaries. The numeric targets, load and wasteload allocations, and Implementation Plan are designed to support and protect the water body’s designated beneficial use of water contact recreation (e.g., swimming and fishing).

7.8.5.1         Problem Statement

Petaluma River and its tributaries are impaired by bacteria. Bacteriological water quality objectives are exceeded based on elevated indicator bacteria densities, and, thus, there is impairment of the water contact recreation (REC-1) beneficial use in these water bodies. Recreating in waters with elevated indicator bacteria densities has long been associated with adverse health effects. Specifically, national epidemiological studies demonstrate that there is a causal relationship between adverse health effects and recreational water quality, as measured by indicator bacteria densities. Impaired segments include the entire Petaluma River, San Antonio Creek, Lichau Creek, Willow Brook, Lynch Creek, Adobe Creek, Ellis Creek, as well as other named and unnamed tributaries.

7.8.5.2         Pollutant Sources

If not properly managed, the following source categories have the potential to discharge bacteria to Petaluma River and its tributaries: municipal wastewater treatment plant, sanitary sewer collection systems, private sewer laterals, onsite wastewater treatment systems (OWTS), vessel marinas, homeless encampments, confined animal facilities (CAF), grazing lands/operations, domestic pets, and municipal and Californian Department of Transportation (Caltrans) stormwater runoff.

7.8.5.3         Numeric Targets

The desired or target condition for the water contact recreation beneficial use in Petaluma River and its tributaries listed in Table 7.8.5-1 are based on protective water quality objectives for fecal indicator bacteria (FIB). These targets are based on applicable water quality objectives for water contact recreation in fresh and marine (estuarine) waters adopted by the State Water Board in the Water Quality Control Plan for Inland Surface Waters, Enclosed Bays, and Estuaries of California.

7.8.5.4         Total Maximum Daily Load

The TMDL is equivalent to the numeric targets in Table 7.8.5-1. The TMDL is expressed as the total density of either E. coli or Enterococcus indicator bacteria, depending on the water body type (freshwater or estuarine), that can be discharged from all sources while not causing the water quality in the river or its tributaries to exceed the protective standards. The “daily” load expression of this TMDL is equivalent to the STV value for Enterococcus and/or E. coli as applicable based on water body type. The TMDL is applicable year-round.

7.8.5.5         Load and Wasteload Allocations

Table 7.8.5-2 summarizes the allocations for discharges of bacteria in the Petaluma River watershed. The load allocations (LAs) and wasteload allocations (WLAs) are the same as the numeric targets specified in Table 7.8.5.1 and the TMDL, except that the allocation for sanitary sewer collection systems, OWTS, and vessel marinas is zero. The allocations are expressed in terms of applicable FIB densities. Discharges to estuarine waters have allocations based on the Enterococcus targets. Discharges to fresh waters have allocations based on the E. coli targets. The “daily” load expression of the WLAs and LAs in Table 7.8.5-2 are equivalent to the appropriate STV, unless the discharge of bacteria is prohibited and the allocation is zero.

The attainment of these allocations will ensure protection of the water quality and applicable beneficial uses of the river. Complete and successful implementation of corrective actions called for in the Implementation Plan may be used to show respective source categories have achieved their LAs or WLAs.

The load allocations in this TMDL are identical to the U.S. EPA criteria and State Water Board water quality objectives established as protective standards. Therefore, the margin of safety is implicitly incorporated into the proposed TMDL and LAs and WLAs. No additional or explicit margin of safety is needed for this TMDL.

While FIB densities can be greater during the winter wet season due to factors such as stormwater runoff, they can be high at any time of year. Recreational uses of the river are most prevalent during the summertime but can occur at any time of year. Therefore, the TMDL and allocations must be applied equally during all time periods and conditions. No seasonal variations to the above listed TMDLs and allocations are proposed.

7.8.5.6         Implementation Plan

The Petaluma River Bacteria TMDL Implementation Plan specifies actions needed to attain the TMDL and allocations. This Implementation Plan includes new actions and actions for which requirements are already in place. The new actions include requirements for the following sources:

• Confined animal facilities not currently enrolled under the Water Board’s CAF Waste Discharge Requirements (WDRs) (e.g., commercial horse boarding facilities);
• Grazing lands/grazing operations not affiliated with existing dairies;
• Vessel marinas;
• Homeless encampments;
• Sanitary sewer collection systems segments within 2000 feet of the river or major tributaries^[1] ;
• OWTS within the Advanced Protection Management Program boundary, within 200 feet of the river or major tributaries; and
• Municipal and Caltrans stormwater runoff.

Actions for which requirements are already in place include:

• Reduction of bacteria discharges from cow dairy facilities by measures required by the CAF WDRs or conditional waiver of CAF WDRs;
• Effluent limitations required by the National Pollutant Discharge Elimination System (NPDES) permit for the City of Petaluma Ellis Creek Wastewater Treatment Facility; and
• Reduction of sanitary sewer waste discharges by the measures already required by the Statewide General WDRs for sanitary sewer systems.

Regulatory Tools
The Water Board will use its regulatory authorities to require actions in the Implementation Plan, including individual and general WDRs under Water Code section 13263; waiver of WDRs under Water Code section 13269; technical or monitoring program reports under Water Code section 13267; NPDES permits for wastewater discharges from sanitary sewer collection systems and treatment facilities and for stormwater discharges from municipal and Caltrans separate storm sewer systems under the Clean Water Act section 402, and Water Code section 13377; and vessel sanitation requirements under the Harbors and Navigation Code section 775 et seq. The Water Board will also use its regulatory authorities in connection with overseeing implementation of the State Water Board’s Water Quality Control Policy for Siting, Design, Operation, and Maintenance of Onsite Wastewater Treatment Systems (OWTS Policy). The Water Board may also enforce the Basin Plan’s prohibition of discharges of raw sewage or any waste failing to meet WDRs to any waters in the Basin.

Implementing Parties
Responsibility for reducing bacteria discharges include the following parties:

• Confined animal facilities owners/operators;
• Grazing lands owners/operators;
• Vessel marina owners/operators;
• OWTS owners within the Advanced Protection Management Program boundary;
• Sonoma County;
• Sonoma County Water Agency (Penngrove Sanitation Zone);
• City of Petaluma;
• Marin County;
• City of Novato; and
• Caltrans.

Achieving the TMDL requires action by all the implementing parties and each is required to meet its pollutant load allocation. Cooperation is encouraged not only to attain the TMDL, but also to avoid duplicative actions, such as monitoring and reporting. To the extent possible, implementing parties should coordinate actions and water quality monitoring efforts.

Implementation Actions and Schedule
This section describes the actions necessary to achieve the TMDL. Tables 7.8.5-3, 7.8.5-4, 7.8.5-5, 7.8.5-6, 7.8.5-7, 7.8.5-8, 7.8.5-9, 7.8.5-10, and 7.8.5-11 set forth the implementation and monitoring actions, lists the implementing parties, and provides the schedule for implementation to achieve the TMDL. The implementation schedule allows time for the implementing parties to identify and implement measures that are necessary to control bacteria discharges resulting in exceedances of allocations. If source control actions are fully implemented throughout the watershed and the TMDL targets are not met, the Water Board may re-evaluate or revise the targets, TMDL, and allocations as appropriate.

The Water Board will adopt WDRs or waivers thereof for grazing operations in the Petaluma watershed, by December 2022, to require those implementation actions listed in Table 7.8.5-8 applicable to grazing lands and operations. Pursuant to Harbors and Navigation Code sections 775 et seq. and Water Code section 13267, the Water Board will require marina owners and operators to comply with the implementation actions listed in Table 7.8.5-6 applicable to vessel marinas. For new implementation actions for sanitary sewer collection systems and municipal separate storm sewer systems listed in Tables 7.8.5-4 and 7.8.5-9, respectively, the Water Board will require the actions through amended or reissued NPDES permits and Water Code sections 13267 and 13383, as necessary. The Water Board will use its stormwater NPDES permitting and Water Code sections 13267 and 13383 authorities to require Table 7.8.5-10 implementation actions related to homeless encampments. General WDRs for sanitary sewer collection systems, general WDRs and a waiver thereof for confined animal facilities, and an NPDES permit for the Ellis Creek Wastewater Treatment Plant exist and Tables 7.8.5-4, 7.8.5-7, and 7.8.5-3, respectively, require ongoing compliance with these requirements. Confined animal facilities not yet covered under these requirements are required to obtain coverage. OWTS implementation actions are further described below.

Advanced Protection Management Program for OWTS
Implementation of actions to eliminate OWTS waste discharges is supported by Prohibition 15 of the Basin Plan (Table 4-1), which prohibits discharges of raw sewage or any waste failing to meet WDRs to any waters of the Basin. In addition, the OWTS Policy provides a multi-tiered strategy for management of OWTS in California. For all OWTS located near a water body that has been listed as impaired due to FIB or nutrients pursuant to Section 303(d) of the Clean Water Act (e.g., Petaluma River and tributaries), an Advanced Protection Management Program (APMP) is the minimum required management program. Local agencies who are responsible for regulating OWTS (e.g., Sonoma and Marin Counties) are authorized to implement APMPs in conjunction with an approved Local Agency Management Program (LAMP). This Implementation Plan establishes APMP requirements for OWTS in the Petaluma River watershed. As required by the OWTS Policy, the relevant local agencies, Sonoma and Marin Counties, shall submit a revised LAMP to the Water Board that includes these TMDL requirements in an appropriate APMP within a year of the TMDL effective date.

Applicability
The APMP applies to OWTS, which are defined as individual disposal systems, community collection and disposal systems, and alternative collection and disposal systems that use subsurface disposal. The APMP applies to any OWTS that is partially or fully contained within the APMP boundary. Owners of existing, new, and replacement OWTS whose OWTS are located entirely outside the boundaries of the APMP are not subject to the APMP requirements, but must still comply with relevant requirements of the OWTS Policy, any approved LAMP, and if applicable, individual and/or general WDRs or waiver of WDRs.

Boundary
The APMP boundary in the Petaluma River watershed includes the following areas:

• The area within 200 linear feet from the top of the bank in the horizontal (map) direction on either side of the entire Petaluma River mainstem; or
• The area within 200 linear feet from the top of the bank in the horizontal (map) direction on either side of any National Hydrography Dataset medium resolution mapped stream in the Petaluma River watershed.

APMP Requirements
Owners of OWTS within the boundaries of the APMP shall comply with the following minimum requirements:

1. General Operation and Maintenance Requirements – Owners of OWTS shall maintain their OWTS in good working condition, including inspections and pumping of solids, as necessary, or as required by local ordinances and requirements established in an approved LAMP, to maintain proper function and assure adequate treatment and disposal.
2. Basic Operational Inspection – To facilitate timely identification and resolution of maintenance and operational issues, owners of OWTS shall obtain a basic operational inspection of the septic tank, effluent dispersal area(s), and related appurtenances of the OWTS by a qualified professional^[2] within three years of the effective date of the TMDL and once every ten years thereafter. Satisfaction of operational inspection requirements may occur in conjunction with pumping of the septic tank, a property transaction, issuance of a local building permit, an infield performance verification performed by a service provider certified by an OWTS manufacturer, or an inspection otherwise required by the local agency or Water Board. A basic operational inspection shall provide sufficient information for the Water Board or local agencies to determine that OWTS are not discharging any waste to the river or its tributaries and may include the following evaluations:


1. Overall system
1. A basic description and layout diagram of the existing system, including the components of the systems, north arrow, assessor’s parcel number, direction of slope, and measurement to relevant features on the property, including any streams or creeks;
2. The units/structures served by the system;
3. Estimated age of the system (both tank and effluent dispersal system);
4. Capacity of the system components (e.g., the volume of the septic tank, the hydraulic capacity of the effluent dispersal area);
5. Availability and condition of the reserve replacement area of the effluent dispersal area; and
6. Inspection of all relevant documents, when available, such as: permits, plans, operation and maintenance manuals, and recent pumpers report (within last 5 years).


2. Septic Tank
1. Tank Water Level
1. Measure liquid elevation with respect to tank interior bottom; and
2. Measure liquid level with respect to inlet and outlet elevations.


2. Tank Solids
1. Measure vertical depth of accumulated settled solids (“sludge”);
2. Measure vertical depth of accumulated floating solids (“scum”); and
3. Estimate total volume of solids present (based on 1 and 2 above.


3. Tank Water-tightness and Integrity
1. Water-tightness: Verify status. Conduct water-tightness test and record results; and
2. Integrity: After pump-out, observe general conditions, including evidence of leaks, cracks, excessive corrosion, inadequate seals, root intrusion, or other integrity compromises.


4. OWTS Components (e.g., distribution box, effluent filter, dosing tank)
1. Describe equipment and current conditions. Describe any evidence of problems.


3. Pump Systems
1. Alarms (if present): Describe equipment and operating condition of all water-level alarms and pump-function alarms; and
2. Pumps (if present): Describe equipment and operating conditions. Review and assess equipment settings, monitoring and operations.


4. Effluent Dispersal Area(s)
1. Investigate dispersal system area and adjacent downhill areas, for any evidence of surfacing effluent;
2. Observe for odors;
3. Inspect distribution box for proper settings and proper operating condition;
4. Observe inspection ports or monitoring wells;
5. Provide depth to groundwater if information is already available; and
6. Conduct a dye test, if one has not been conducted in the past five years.


5. Supplement Treatment or Custom-Designed Systems
1. The requirements of a basic inspection for OWTS utilizing supplemental treatment components and/or enhanced effluent distribution systems will depend on the type of individual OWTS. Applicable inspection protocol will include obtaining the information described here for all OWTS. It will include inspection requirements specified by the appropriate local agency’s permits for the OWTS, and as otherwise dressed in Local Agency OWTS codes and regulations.

3. Need for Corrective Action – In addition to conditions requiring corrective action set forth in section 11.0 of the OWTS Policy, OWTS meeting any of the following criteria are also deemed to be in need of corrective action and must be replaced, repaired, or modified so as to comply with requirements of an approved LAMP, WDRs, or a waiver of WDRs:
   1. OWTS discharging to the ground surface or surface waters;
   2. OWTS that do not include a septic tank and an effluent dispersal system that complies with the OWTS Policy; and
   3. OWTS with projected wastewater flow exceeding the capacity of one or more components of the treatment and disposal system.

Water Board OWTS Assessment Program
The Water Board will conduct an initial OWTS assessment to identify OWTS that are failing and/or in need of corrective action. The Water Board will assess all OWTS within the boundaries of the APMP to determine whether the OWTS is failing and/or in need of corrective action. The assessment will primarily rely on the results of the basic operational inspection performed by a qualified professional. It may also include a desktop or local record review. Information that may be used to ascertain the performance of an existing OWTS includes, but is not limited to, the OWTS type, age, approved variances, repair history, monitoring and inspection results, septic tank pumping records, maintenance records, peak hydraulic loading, and record of any uncorrected deficiencies or substantiated complaints received.

To obtain information for the OWTS assessment, the Water Board will work with local agencies to obtain records pertaining to OWTS and building permits from each local agency within three months of the TMDL effective date. It will also require each property owner within the APMP boundary to submit a basic operational inspection report to the Water Board within three years of the effective date of the TMDL. To do so, the Water Board will issue Water Code section 13267 Orders to homeowners within six months of the TMDL effective date. The Water Board staff will screen the inspection reports to classify the OWTS into three categories as follows:

• Category 1 - Acceptable^[3] : no actions needed;


• Category 2 - Needing Possible Follow Up^[4] : Within two years after receiving the basic operational inspection report, the Water Board will review, prioritize, and recommend a schedule for corrective actions commensurate with the level of threat to water quality. The level of threat to water quality will be determined based on parameters such as system’s age, proximity to waters, expansion without septic permit records. If Water Board staff determine that an OWTS in this category is in need of corrective actions, the Water Board staff will identify the appropriate corrective action, set an appropriate time schedule for compliance that is not more than 12 years from the TMDL effective date, notify the property owner of the requirement to contact the local agency to obtain appropriate local agency permit(s) and initiate the corrective actions, and rely on Water Board enforcement authorities, if necessary; and


• Category 3 - Needing Major Repair^[5] : The Water Board will report these systems to local agencies for immediate initiation of permitting process and corrective actions. The Water Board expects that all OWTS in this category will be treated by the local agencies as an immediate risk to public health. The local agencies are the lead for contacting the landowner to require corrective actions, setting an appropriate time schedule for compliance that shall be commensurate with the risk, and taking enforcement actions as necessary. The time schedule for compliance in no case shall be more than 12 years from the TMDL effective date.

OWTS Requiring Corrective Actions
Property owners with OWTS within the boundaries of the APMP that require corrective action are subject to Tier 4^[6] (“OWTS requiring corrective actions”) of the OWTS Policy and must follow the requirements as specified in Section 11 of the Policy. Property owners who are required to upgrade, repair, or replace an existing OWTS or acquire a new OWTS must obtain the appropriate local agency permit in accordance with the local agency’s ordinances and policies. The local agencies are the lead organization for plan review, local permit issuance, construction inspection, monitoring of new and upgraded OWTS (if applicable), and overseeing repairs or replacement of existing OWTS, as provided in their permitting and enforcement process.

Local agencies shall track and report status of corrective actions for Category 2 systems on an annual basis, and for Category 3 systems (major repairs) on a quarterly basis. The local agencies shall incorporate these reporting timelines into their respective APMPs.

If an owner fails to comply with the corrective action requirements of Tier 4 of the OWTS Policy, the OWTS discharges will no longer be covered under the OWTS Policy’s waiver of WDRs. The Water Board may require such an owner to submit a report of waste discharge for evaluation on a case-by-case basis and/or take appropriate enforcement action.

This Implementation Plan does not affect or supersede any more stringent local requirements.

7.8.5.7         Water Quality Monitoring

The implementing parties are responsible for developing and implementing a comprehensive monitoring plan to accomplish the following goals: 1) better characterize FIB contributions from their sources/jurisdictions, 2) assess best management practices (BMP) effectiveness, and 3) assess progress towards attainment of their respective LAs and WLAs. Relying on Water Code section 13267, the Water Board will require the implementing parties to submit a monitoring plan for achieving these goals within one year of the TMDL effective date. Where possible, the implementing parties may collaboratively develop and implement a joint monitoring plan. Implementing parties shall provide monitoring data (e.g., FIB, MST, or other relevant data) to the Water Board to determine if their implementation actions have resulted in achieving their respective LAs or WLAs.

The CAF permittees are still required to comply with the monitoring requirements of the Water Board’s CAF Order. However, in lieu of the TMDL FIB water quality monitoring, CAFs and grazing operations may demonstrate attainment of their LAs through sampling of other indicator parameters (e.g., ammonia) or by demonstrating they have implemented all required implementation measures for addressing bacteria discharges from their respective source categories and are in full compliance with their respective WDRs. However, if these entities are found to be noncompliant with their orders, the Water Board may also require them to develop and implement a water quality monitoring program as described above.

For the OWTS source category, the Water Board will track and use proof of required corrective actions taken by the property owners as evidence that they have achieved the LA. No additional water quality monitoring is required for this source category to demonstrate attainment of the LA.

The Water Board will collect water quality data to evaluate whether TMDL targets are attained throughout the Petaluma River watershed. Sampling will occur after significant implementation actions have been taken in the watershed. Specifically, it will collect data every five years, starting after the effective date of the TMDL. Sampling stations will be identified at a number of major tributaries and along the river’s main stem at locations associated with particular sources and locations where previous water quality data were collected to identify water quality trends.

7.8.5.8         Agricultural Water Quality Control Program Costs

The implementation measures for grazing lands and dairies constitute an agricultural water quality control program and, therefore, consistent with California Water Code section 13141 requirements, the cost of the program is estimated herein. The total program implementation cost for this agricultural source category is estimated to range between $131,000 and $209, 000 per year over the next 10 years. The estimated cost will be shared by approximately 190 grazing lands operators within the Petaluma River watershed. This estimate includes the costs of implanting animal waste control and grazing management measures and is based on costs associated with technical assistance and evaluation, installation of water troughs, and cattle control fencing along streams. The program cost estimate may be high as it does not account for implementation measures that ranchers have already implemented. Further, besides fencing, other acceptable methods of managing livestock access to streams are not included in this cost estimate due to variability in costs and site-specific applicability. Potential financing sources to implement this program include federal and state water quality grants and federal agricultural grants such as those provided by the Nonpoint Source Implementation Grants (319 Program) and United States Department of Agriculture Natural Resources Conservation Service.

7.9 Water Quality Attainment Strategies and TMDLs for the Suisun Basin (see Figure 2-9)

7.9.1 Suisun Marsh Low Dissolved Oxygen/Organic Enrichment TMDL

The following sections establish the TMDL for dissolved oxygen (DO) in Suisun Marsh wetlands. The numeric targets, allocations, and implementation plan are designed to attain the numeric water quality objectives set forth in Section 3.3.5, reduce occurrences of anthropogenically-induced low DO in Suisun Marsh wetlands, specifically in sloughs and channels, and protect beneficial uses for aquatic life (i.e., EST, MIGR, RARE, and SPWN).

7.9.1.1         Problem Statement

Low DO events resulting from environmental conditions and management actions in some managed wetlands adversely impact the aquatic life beneficial uses in Suisun Marsh. These problems are particularly evident in the slow-flowing, low-mixing, back-end sloughs that dominate the western portion of the marsh. In fall, these sloughs experience low DO conditions caused by bacterial decomposition of vegetation in managed wetlands (e.g., duck clubs), leading to surface water that is anaerobic or has low levels of DO. When this water is drained from managed wetland properties, receiving waters in sloughs become degraded. Fish kills were observed in the western marsh with associated low DO conditions between 2000 and 2009. The extent of the environmental impacts of water released from managed wetlands depends on the residence time of the low DO water in the receiving water. Residence time is dependent on the amount of tidal circulation within the sloughs. Large tidal sloughs, such as Montezuma or Nurse sloughs, exchange water rapidly and thus are not as prone to low DO problems. Small and especially dead-end sloughs experience less tidal exchange and longer residence times and, consequently, are particularly susceptible to low DO problems.

This TMDL focuses on resolving DO impairment of named and unnamed sloughs and channels in the western part of Suisun Marsh, including but not limited to Peytonia, Boynton, Sheldrake, Cordelia, and Goodyear sloughs.

7.9.1.2         Numeric Targets

The TMDL targets in Table 7.9.1-1 are the water quality objectives for dissolved oxygen designed to protect sensitive fish and invertebrates, thereby generally protecting aquatic organisms in Suisun Marsh sloughs and channels.

The acute DO objective (3.8 mg/L) ensures protection of juvenile and adult fish survival, and the chronic objective (5 mg/L) ensures protection of larval and juvenile growth effects under long-term exposure. The 6.4 mg/L chronic objective protects listed juvenile salmonids using the marsh as a migratory path. The acute objective is attained when the average daily DO concentrations are at or above 3.8 mg/L, and the chronic objectives are attained when average monthly (30-day) DO concentrations are at or above 5.0 mg/L or 6.4 mg/L in the applicable waterbodies. Continuous data collected at regular intervals (every 15 to 60 minutes) are needed to fully evaluate whether the objectives are met. A daily average is the arithmetic average of all DO measurements collected within a 24-hour period. The 30-day running average is the arithmetic average of daily averages for any 30 consecutive days. Each subsequent 30-day average is computed by sliding the averaging window by one day. Attainment of these objectives will ensure that conditions in the sloughs support the most sensitive aquatic life beneficial uses present.

7.9.1.3         Sources

Low dissolved oxygen is a common aquatic system response to elevated organic matter inputs. Tidal marshes and managed wetlands are naturally rich in organic matter due to the growth of wetland plants and their subsequent decay, which consumes oxygen. The natural tendency for organic enrichment in wetland environments is exacerbated in Suisun Marsh due to wetland management activities. Flooding and draining cycles and vegetation management practices at managed wetlands induce releases of organic carbon from wetland soils and vegetation beyond what would naturally occur. Other sources of organic oxygen demanding substances (carbon and nutrients) include the treated wastewater discharge from the FairfieldSuisun Sewer District treatment plant (municipal wastewater), municipal stormwater runoff, and natural biotic processes in the marsh.

7.9.1.4         Total Maximum Daily Load and Allocations

The TMDL is equivalent to the TMDL targets in Table 7.9.1-1. The TMDL allocations are summarized in Table 7.9.1-2. These allocations apply year-round. Marsh landowners, the Suisun Resource Conservation District (SRCD), California Department of Fish and Wildlife (CDFW), California Department of Water Resources (DWR), and U.S. Bureau of Reclamation (USBR) are collectively responsible for meeting the managed wetlands allocations.

7.9.1.5         Implementation Plan

The Suisun Marsh wetlands provide habitat for dozens of fish and aquatic invertebrate species, as well as a variety of resident and migratory waterfowl and shorebirds. The intended outcome of the implementation plan is to improve habitat conditions for aquatic organisms and wildlife and to minimize or avoid adverse effects of low DO concentrations. This implementation plan provides directions for implementing the TMDL and allocations and focuses on the following:

• Actions to control internal sources of low DO at managed wetlands;
• Actions to control external sources of low DO from municipal wastewater and municipal stormwater runoff; and
• Actions resulting from Estuary-wide plans and policies.

Internal sources at managed wetlands

Load allocations from managed wetlands will be implemented through Clean Water Act section 401 certifications and/or waste discharge requirements issued to responsible parties to attain DO concentrations in sloughs receiving discharges from managed wetlands. The Water Board will continue to require implementation of best management practices (BMPs) and DO monitoring in sloughs to attain the load allocations as part of the 401 certification of the U.S. Army Corps of Engineers’ Regional General Permit (RGP). The RGP authorizes managed wetland operation and maintenance activities, including levee stability improvements and maintenance of water control facilities and structures in the marsh. These activities are conducted by private land owners and public entities (CDFW, DWR, and USBR) and coordinated by SRCD. All aforementioned entities are collectively responsible for implementing the provisions required by the 401 certification to achieve the load allocations. The RGP also authorizes the cleaning of interior ditches, including the Goodyear Slough outfall managed by DWR. Maintaining good flow circulation in Goodyear Slough is essential to improving DO conditions in the western marsh. DWR is responsible for conducting the cleaning of the outfall as often as necessary to maintain water circulation and specifically should inspect and clean the outfall before the fall flood up begins at the managed wetlands.

Understanding of DO conditions across the entire marsh slough complex will improve with additional monitoring data over time and space. The information gained through the implementation of BMPs at the managed wetlands in the western portion of the marsh will be used to refine selection and deployment of BMPs in the future. As a result of adaptive management and monitoring, additional implementation of BMPs could be required in the western marsh or elsewhere depending on implementation progress or if water quality conditions decline in the eastern marsh.

External sources: municipal stormwater runoff and municipal wastewater

Municipal stormwater runoff and municipal wastewater discharges have been identified as potential sources of organic material into the marsh sloughs and a potential conveyer of other pollutants that may affect DO (e.g., nutrients). This TMDL does not require new implementation actions because the existing regulatory programs for municipal stormwater runoff and municipal wastewater are in place and will continue to address mercury and dissolved oxygen.

The wasteload allocations for municipal stormwater shall be implemented through the Municipal Regional Stormwater NPDES permit (MRP) as receiving water limitations. These allocations apply to the City of Fairfield and Suisun City.

The wasteload allocation for the FSSD wastewater treatment plant shall be implemented through its NPDES permit as receiving water limitations.

Estuary-wide plans and policies

Future large-scale tidal marsh restoration efforts, mitigation projects, and new flow and salinity objectives for the Delta and Sacramento and San Joaquin Rivers may result in a more productive aquatic food web in Suisun Marsh and in localized and system-wide changes to DO concentrations. The Water Board will work with the State Water Board and other State and federal agencies managing Suisun Marsh to protect fish and wildlife beneficial uses and to better manage and improve water quality in Suisun Marsh.

Evaluation and Monitoring

Implementing parties are responsible for developing monitoring plans and conducting monitoring sufficient to assess compliance with the wasteload allocations, load allocations, and DO numeric targets established for Suisun Marsh sloughs. SRCD, together with the managed wetland owners and other agencies (CDFW, DWR, USBR), are required to conduct DO monitoring in the sloughs receiving discharge from managed wetlands, including continuous DO monitoring at compliance points, in order to evaluate whether they are achieving the load allocation and site specific objectives. These entities shall report monitoring results annually to the Water Board, document their efforts to improve water quality, describe the BMPs implemented during the fall discharge period, and coordinate details among adjacent managed wetlands, with a focus on efforts in the western marsh.

The Water Board will collaborate with other agencies, especially DWR, which operates a network of monitoring sites for the purpose of mitigating adverse impacts on salinity from the State Water Project and Central Valley Project, to identify opportunities to collect additional DO data in Suisun Marsh sloughs. This information will be used to enhance our understanding of DO variability and the extent to which deviations from the DO objectives occur under natural and anthropogenic conditions.

The MRP shall continue to require monitoring of DO to identify stormwater pollutant sources and to evaluate attainment of water quality objectives in receiving waters.

The FSSD NPDES permit shall continue to require monitoring of DO in receiving waters and implementation of BMPs to maintain optimal treatment performance in relation to DO.

The National Estuarine Research Reserve (NERR) conducts water quality monitoring in the First and Second Mallard sloughs, which represent minimally impacted tidal sloughs. Continued data collection by NERR will assist the Water Board in evaluating the potential effects of climate on the marsh and trends in DO conditions.

 

FIGURES

Figure 7.2.1-1  Segments of San Francisco Bay showing location of Hayward Shoals as a line connecting Little Coyote Point and the Oakland Airport.

TABLES

7.1.1 Water Quality Attainment Strategy and TMDL for Diazinon and Pesticide-related Toxicity in Urban Creeks

Table 7.1.1-1   Benchmark Factors
Table 7.1.1-2:  Water Board Implementation Measure Tracking

7.2.1 Water Quality Attainment Strategy to Support Copper Site-specific Objectives for San Francisco Bay, and Nickel Site-specific Objectives for South San Francisco Bay

Table 7.2.1-1   Translators Applicable to South San Francisco Bay Municipal Wastewater Discharges for Copper and Nickel
Table 7.2.1-2   Translators Applicable to Other San Francisco Bay Municipal and Industrial Wastewater Deep Water Discharges for Copper
Table 7.2.1-3   Dissolved Copper (μg/L) Trigger Concentrations at 99% Statistical Power

7.2.2 San Francisco Bay Mercury TMDL

Table 7.2.2-1   Mercury Load and Wasteload Allocations By Source Category
Table 7.2.2-2   Individual Wasteload Allocations for Mercury in Urban Stormwater Discharges
Table 7.2.2-3   Individual Wasteload Allocations for Mercury in Municipal Wastewater Discharges
Table 7.2.2-4   Individual Wasteload Allocations for Mercury in Petroleum Refinery Wastewater Discharges
Table 7.2.2-5   Individual Wasteload Allocations for Mercury in Industrial (Non-Petroleum Refinery) Wastewater Discharges

7.2.3 San Francisco Bay Polychlorinated Biphenyls TMDL

Table 7.2.3-1   PCBs Sources and Current Loads to San Francisco Bay
Table 7.2.3-2   Load and Wasteload Allocations
Table 7.2.3-3   Individual Wasteload Allocations For Municipal Wastewater Dischargers
Table 7.2.3-4   Individual Wasteload Allocations for Industrial Wastewater Dischargers
Table 7.2.3-5   County-Based Watershed Wasteload Allocations for Stormwater Runoff

7.2.4 North San Francisco Bay Selenium Total Maximum Daily Load (TMDL)

Table 7.2.4-1   Numeric Targets for Selenium
Table 7.2.4-2   Selenium Load Allocation
Table 7.2.4-3   Individual Wasteload Allocations for Petroleum Refineries
Table 7.2.4-4   Individual Wasteload Allocations for Municipal and Industrial Dischargers

7.2.5 San Francisco Bay Beaches Bacteria TMDL

Table 7.2.5-1   Numeric Targets for San Francisco Bay Beaches
Table 7.2.5-2   Load and Wasteload Allocations for San Francisco Bay Beaches
Table 7.2.5-3   Implementation Plan Elements
Table 7.2.5-4   Aquatic Park Beach Implementation Plan
Table 7.2.5-5   Candlestick Point Beaches Implementation Plan
Table 7.2.5-6   Crissy Field Beach Implementation Plan
Table 7.2.5-7   Marina Lagoon Beaches (Parkside Aquatic and Lakeshore) Implementation Plan

7.3.1 Tomales Bay Watershed Pathogens TMDL

Table 7.3.1-1   Water Quality Targets for Tomales Bay and Its Tributaries
Table 7.3.1-2   Total Maximum Daily Load of Pathogens Indicators for Tomales Bay and its Tributaries
Table 7.3.1-3   Density-Based Pollutant Wasteload and Load Allocations for Dischargers of Pathogens in Tomales Bay Watershed
Table 7.3.1-4   Density-Based Pollutant Load Allocations for Tomales Bay Tributaries
Table 7.3.1-5   Trackable Implementation Measures for the Tomales Bay Watershed Pathogens Total Maximum Daily Load
Table 7.3.1-6   Regulatory Framework for Discharges by Source Category
Table 7.3.1-7   Baseline Water Quality Monitoring Program

7.3.2 Total Maximum Daily Load for Mercury in Walker Creek and Soulajule Reservoir

Table 7.3.2-1   TMDL Mercury Wasteload and Load Allocations
Table 7.3.2-2   Implementation Measures for Walker Creek Mercury TMDL
Table 7.3.2-3   Baseline Monitoring Sites

7.3.3 Lagunitas Creek Sediment TMDL

Table 7.3.3-1   Sediment and Habitat Targets for the Lagunitas Creek and its Tributaries
Table 7.3.3-2   Mean Annual Sediment Delivery to Lagunitas Creek upstream of Devils Gulch (drainage area = 89 km²) during water years 1983 through 2008
Table 7.3.3-3   Mean Annual Sediment Delivery to Lagunitas Creek upstream of Olema Creek (drainage area = 213 km²) during water years 1983 through 2008
Table 7.3.3-4   Load Allocations for Sediment Discharges for Lagunitas Creek Upstream of Devils Gulch
Table 7.3.3-5   Load Allocations for Sediment Discharges for Lagunitas Creek Upstream of Olema Creek
Table 7.3.3-6   Wasteload Allocations for Stormwater for Lagunitas Creek Upstream of Olema Creek
Table 7.3.3-7   TMDL Implementation Measures for Sediment Discharges Associated with Point Sources
Table 7.3.3-8   Required TMDL Implementation Measures for Sediment Discharges Associated with Grazing
Table 7.3.3-9   Required TMDL Implementation Measures for Sediment Discharges associated with Parks and Open Space and/or Municipal Public Works
Table 7.3.3-10   Actions to Enhance Habitat Complexity and Connectivity in Lagunitas Creek and its Tributaries
Table 7.3.3-11   Goals for Floodplain Restoration and/or Large Woody Debris Enhancement in Lagunitas Creek Watershed

7.4.1 San Pedro Creek and Pacifica State Beach Bacteria TMDL

Table 7.4.1-1   Bacteriological Water Quality Objectives for San Pedro Creek and Pacifica State Beach
Table 7.4.1-2   Numeric Targets, TMDLs, and Allocations Based on Allowable Exceedances of Single-Sample Objectives for San Pedro Creek and Pacifica State Beach
Table 7.4.1-3   Load and Wasteload Allocations for Dischargers of Bacteria in San Pedro Creek Watershed
Table 7.4.1-4   Implementation Plan Requirements and Schedule

7.4.2 Pescadero-Butano Watershed Sediment TMDL and Habitat Enhancement Plan

Table 7.4.2-1   Sediment TMDL and Habitat Targets for Pescadero and Butano Creeks and Their Tributaries
Table 7.4.2-2   Mean Annual Sediment Delivery to the Pescadero-Butano Watershed (tons/year)
Table 7.4.2-3   Load Allocations
Table 7.4.2-4   Wasteload Allocations for Stormwater Runoff
Table 7.4.2-5   TMDL Implementation Measures for Sediment Discharges Associated with Stormwater Runoff and Roads
Table 7.4.2-6   Required TMDL Implementation Measures for Sediment Discharges Associated with Non-Grazing Agricultural Lands of 5 Acres or Greater
Table 7.4.2-7   Required TMDL Implementation Measures for Sediment Discharges Associated with Grazing Lands of 50 Acres or Greater
Table 7.4.2-8   Required TMDL Implementation Measures for Sediment Discharges associated with San Mateo County
Table 7.4.2-9   Required TMDL Implementation Measures for Sediment Discharges associated with Parks and Open Space Lands
Table 7.4.2-10   Required TMDL Implementation Measures for Sediment Discharges Associated with Timber Lands of 100 acres or Greater
Table 7.4.2-11   Recommended Actions to Reduce Sediment Load and Enhance Habitat Complexity in Pescadero and Butano Creeks and Their Tributaries

7.4.3 Bacteria TMDL for Beaches in Pillar Point Harbor and Venice Beach

Table 7.4.3-1   Numeric Targets to Protect Water Contact Recreation in Pillar Point Harbor Beaches and Venice Beach
Table 7.4.3-2   Load and Wasteload Allocations of Indicator Bacteria for Beaches at Pillar Point Harbor and Venice Beach
Table 7.4.3-3   Implementation Actions and Schedule for SAM Treatment Plant
Table 7.4.3-4   Phase 1 Implementation Actions and Schedule for Sanitary Sewer Collection Systems
Table 7.4.3-5   Phase 2 Implementation Actions and Schedule for Sanitary Sewer Collection Systems
Table 7.4.3-6   Implementation Actions and Schedule for Ox Mountain Landfill
Table 7.4.3-7   Phase 1 Implementation Actions and Schedule for Vessels and Amenities in Pillar Point Harbor
Table 7.4.3-8   Phase 2 Implementation Actions and Schedule for Vessels and Amenities in Pillar Point Harbor
Table 7.4.3-9   Phase 1 Implementation Actions and Schedule for Municipal Stormwater Runoff
Table 7.4.3-10   Phase 2 Implementation Actions and Schedule for Municipal Stormwater Runoff
Table 7.4.3-11   Implementation Actions and Schedule for Caltrans
Table 7.4.3-12   Implementation Actions and Schedule for Existing, New and Replacement Onsite Wastewater Treatment Systems (OWTS)
Table 7.4.3-13   Implementation Actions and Schedule for CAFs

7.5.1 Richardson Bay Pathogens Total Maximum Daily Load (TMDL)

Table 7.5.1-1   Numeric Targets for Richardson Bay
Table 7.5.1-2   Total Maximum Daily Load for pathogen indicators (fecal coliforms) for Richardson Bay
Table 7.5.1-3   Density-Based Pollutant Wasteload and Load Allocations for Richardson Bay
Table 7.5.1-4   Trackable implementation measures for the Richardson Bay pathogens TMDL
Table 7.5.1-5   Regulatory Framework

7.7.1 Total Maximum Daily Loads for Mercury in Waters of the Guadalupe River Watershed

Table 7.7.1-1   Total Maximum Daily Loads
Table 7.7.1-2   Load and Wasteload Allocations

7.8.1 Sonoma Creek Pathogens Total Maximum Daily Load (TMDL)

Table 7.8.1-1   Water Quality Targets for Sonoma Creek
Table 7.8.1-2   Total Maximum Daily Loads of Pathogen Indicators for Sonoma Creek
Table 7.8.1-3   Density-Based Pollutant Load and Wasteload Allocations for Dischargers of Pathogens in the Sonoma Creek Watershed
Table 7.8.1-4   Trackable Implementation Measures for the Sonoma Creek Pathogen Total Maximum Daily Load
Table 7.8.1-5   Regulatory Framework for Discharges by Source Category
Table 7.8.1-6   Baseline Monitoring Sites

7.8.2 Napa River Pathogens Total Maximum Daily Load (TMDL)

Table 7.8.2-1   TMDL Water Quality Targets for the Napa River
Table 7.8.2-2   Total Maximum Daily Loads of Pathogen Indicators for the Napa River
Table 7.8.2-3   Density-Based Pollutant Load Allocations and Wasteload Allocations for Pathogen Dischargers in the Napa River Watershed
Table 7.8.2-4   Density-Based Wasteload Allocations for Municipal Wastewater Treatment Facilities
Table 7.8.2-5   Trackable Implementation Measures for the Napa River Pathogen Total Maximum Daily Load
Table 7.8.2-6   Regulatory Framework for Discharges by Source Category
Table 7.8.2-7   Baseline Monitoring Sites

7.8.3 Sonoma Creek Watershed Sediment TMDL and Habitat Enhancement Plan

Table 7.8.3-1 TMDL Sediment Targets for Sonoma Creek and its Tributaries
Table 7.8.3-2. Average Annual Sediment Delivery to Sonoma Creek (tons/year)
Table 7.8.3-3. Sonoma Creek Sediment Load and Wasteload Allocations (tons/year)
Table 7.8.3-4 Required and Trackable TMDL Implementation Measures for Sediment Discharges Associated with Vineyards
Table 7.8.3-5 Required TMDL Implementation Measures for Sediment Discharges Associated with Grazing
Table 7.8.3-6 Required TMDL Implementation Measures for Sediment Discharges Associated with Rural Lands
Table 7.8.3-7 Required TMDL Implementation Measures for Sediment Discharges associated with Parks
and Open Space, and/or Municipal Public Works
Table 7.8.3-8 Required TMDL Implementation Measures for Sediment Discharges associated with Urban Land Uses
Table 7.8.3-9 Recommended Actions to Reduce Sediment Load and Enhance Habitat Complexity in Sonoma Creek and its Tributaries
Table 7.8.3-10 Recommended Actions to Protect or Enhance Baseflow
Table 7.8.3-11 Recommended Actions to Restore to Fish Passage

7.8.4 Napa River Sediment Reduction and Habitat Enhancement Plan

Table 7.8.4-1 TMDL sediment targets for the Napa River and its Tributaries
Table 7.8.4-2. Mean Annual Sediment Delivery to Napa River at Soda Creek (1994-2004)
Table 7.8.4-3a. Load Allocations
Table 7.8.4-3b Wasteload Allocations for Urban Runoff and Wastewater Discharges
Table 7.8.4-4 TMDL Implementation Measures for Sediment Discharges Associated with Urban Stormwater Runoff and Wastewater Discharges
Table 7.8.4-4a Required and Trackable TMDL Implementation Measures for Sediment Discharges Associated with Vineyards
Table 7.8.4-4b Required TMDL Implementation Measures for Sediment Discharges Associated with Grazing
Table 7.8.4-4c Required TMDL Implementation Measures for Sediment Discharges Associated with Rural Lands
Table 7.8.4-4d Required TMDL Implementation Measures for Sediment Discharges associated with Parks
and Open Space, and/or Municipal Public Works
Table 7.8.4-5a Recommended Actions to Reduce Sediment Load and Enhance Habitat Complexity in Napa River and its Tributaries
Table 7.8.4-5b Recommended actions to protect or enhance baseflow Table 7.8.4-5c Recommended Actions to Restore to Fish Passage
Table 7.8.4-5d Recommended Actions to Protect and/or Enhance Stream Temperature

7.8.5 Petaluma River Bacteria Total Maximum Daily Load (TMDL)

Table 7.8.5-1 Numeric Targets for Fecal Indicator Bacteria in the Petaluma River Watershed to Protect Water Contact Recreation
Table 7.8.5-2 Load and Wasteload Allocations of Fecal Indicator Bacteria for Petaluma River
Table 7.8.5-3 Implementation Actions and Schedule for Ellis Creek Wastewater Treatment Plant
Table 7.8.5-4 Implementation Actions and Schedule for Sanitary Sewer Collection Systems
Table 7.8.5-5 Implementation Actions and Schedule for Existing, New, And Replacement Onsite Wastewater Treatment Systems
Table 7.8.5-6 Implementation Actions and Schedule for Vessel Marinas
Table 7.8.5-7 Implementation Actions and Schedule for Confined Animal Facilities
Table 7.8.5-8 Implementation Actions and Schedule for Grazing Lands/ Operations
Table 7.8.5-9 Implementation Actions and Schedule for Municipal Stormwater Runoff
Table 7.8.5-10 Implementation Actions and Schedule for Homeless Encampments
Table 7.8.5-11 Implementation Actions and Schedule for Water Quality Monitoring

7.9.1 Suisun Marsh Low Dissolved Oxygen/Organic Enrichment TMDL

Table 7.9.1-1 Numeric Targets and TMDL for Suisun Marsh
Table 7.9.1-2 Wasteload and Load Allocations