7.3 Water Quality Attainment Strategies and TMDLs for the Marin Coastal Basin (see Figure 2-3)7.3.1 Tomales Bay Watershed Pathogens TMDLThe 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 StatementMonitoring 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:
7.3.1.2 SourcesIf 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.
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 TargetsTable 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 LoadTable 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 AllocationsTMDL 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 PlanThe 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).
Agricultural Water Quality Control Program CostsThe 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 MonitoringDischargers, 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:
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 ImplementationApproximately 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.
7.3.2 Total Maximum Daily Load for Mercury in Walker Creek and Soulajule ReservoirWalker 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 StatementWalker Creek and Soulajule Reservoir are impaired because mercury adversely affects beneficial uses, including wildlife habitat and all uses supporting aquatic life.
7.3.2.2 SourcesThe following sources have the potential to discharge mercury to surface waters in the Walker Creek watershed:
7.3.2.3 TMDL Targets
7.3.2.4 Allocations and Total Maximum Daily LoadThe 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 PlanThe 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 ProgramBecause 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 MonitoringWater 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:
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 ImplementationApproximately 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.
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 PlanThe following sections establish:
The goals of the Lagunitas Creek Sediment Reduction and Habitat Enhancement Plan (Plan) are as follows:
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 StatementDue 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 TargetsIncreased 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 SourcesField 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:
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 AllocationsThe 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 PlanThe 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 ToolsThe 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 SedimentThe 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:
Actions to Enhance Stream-Riparian Habitat Complexity and ConnectivityAlthough 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 CostsImplementation 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 MonitoringThree types of monitoring are specified to assess progress toward achievement of numeric targets and load allocations for sediment:
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 ImplementationIn 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 TMDLThe 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
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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:
- 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].
- 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.
- 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.
- Monitor to evaluate the following:
- effectiveness of erosion control measures
- mercury loads discharged annually to waters of the State at the points of discharge
- fish bioaccumulation of mercury in waters downstream of the discharge
- mercury loads discharged annually to San Francisco Bay, and
- 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:
- 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)
- Monitoring of mercury load at the points of discharge to demonstrate progress in reducing loads (applicable to mercury mines, and reservoirs and lakes)
- Fish tissue mercury monitoring to assess progress in attaining targets
(applicable to mercury mines, and reservoirs and lakes) - 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)
- 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.
- 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?
- 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.
- 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?
- 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 (Tables 3-1 and 3-2). 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.
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 (Tables 3-1 and 3-2). 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:
- Reduce sediment loads, and fine sediment in particular, to Sonoma Creek and its tributaries
- Attain and maintain suitable gravel quality in freshwater reaches of Sonoma Creek and its tributaries
- Reduce and prevent channel incision
- Reduce erosion and sedimentation
- Repair large sources of sediment supply (e.g., landslides)
- Enhance channel complexity (e.g., by adding and encouraging retention of large woody debris and restoring riparian vegetation)
The following sections establish:
- 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
- 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:
- 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.
- 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.
- 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:
- 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.
- 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.
- 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.
- 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.
- 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:
- The bankfull channel width-to depth ratio is > 12:1.
- The average spacing between alluvial and/or forced gravel bars within the active channel is < 7 times the width of the bankfull channel.
- Available shear stress at bankfull flow does not exceed the amount required to initiate motion of the streambed by more than approximately 20 percent.
- Floodplain width is > 4 times bankfull channel width.
Monitoring should also assess whether there is:
- An increasing trend through time in the mean area and frequency of riffles and gravel bars within the mainstem channel; and
- 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:
- 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
- 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:
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.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.
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:
- 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.
- 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.
- Channel sediment loads vary greatly depending upon nature of underlying bedrock or sediment deposits, land use activities, and the location of dams.
- 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/year147,000 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 (http://www.dfg.ca.gov/biogeodata/cnddb/).
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:
- Implementation monitoring to document that required sediment control and habitat enhancement actions are implemented
- Upslope effectiveness monitoring to evaluate effectiveness of sediment control actions in reducing rates of sediment delivery to channels
- 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.
7.9 Water Quality Attainment Strategies and TMDLs for the Suisun Basin (see Figure 2-9)
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FIGURES
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
7.5.1 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 TributariesTable 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
