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

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

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


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

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

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

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

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

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


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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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


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

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

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

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

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


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

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

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