The Bay Delta Water Quality Control Plan sets the water quality objectives meant to protect beneficial uses as well as the Delta’s ecosystem. The plan, last updated in 2006, is currently undergoing major revisions. Here’s a guide to the process underway at the State Water Board.
Protecting the San Francisco Bay/Sacramento-San Joaquin Delta (Bay-Delta) watershed and its many beneficial uses is one of the State Water Board’s primary responsibilities and top priorities. The State Water Board is responsible for adopting and updating the Bay-Delta Water Quality Control Plan (Bay-Delta Plan) to protect beneficial uses in the watershed.
The water quality control planning process
The ‘San Francisco Bay/Sacramento-San Joaquin Delta Estuary Water Quality Control Plan,’ blessedly known as the ‘Bay-Delta Plan’ for short, identifies existing and potential beneficial uses of water and then establishes water quality objectives to protect those uses. The State Water Board is the agency responsible for developing and modifying the Bay-Delta Plan under the authority of the Federal Clean Water Act and the state’s Porter-Cologne Water Quality Control Act.
State law requires the State Water Board and the Regional Water Quality Control Boards to adopt Water Quality Control Plans that include measures to protect water quality in the state’s streams, rivers, and lakes.
The State Water Board protects water quality in the Bay-Delta in part through the Bay-Delta Plan. The Bay-Delta Plan identifies beneficial uses of water to be protected in the Bay-Delta, including municipal and industrial, agricultural, fish and wildlife, water quality and flow objectives to reasonably protect the beneficial uses, and a program of implementation to achieve the objectives. The implementation plan includes actions that the State Water Board will take, such as implementing flow requirements, and actions the State Water Board will take with others or recommending actions to others that they should take, such as habitat restoration. The Bay-Delta Plan also identifies monitoring and assessment measures to evaluate compliance and effectiveness of implementation actions.
The Regional Water Quality Control boards adopt Water Quality Control Plans or basin plans to protect beneficial uses of water according to state and federal law. Two Regional Water Quality Control Board basin plans include water bodies in the Bay-Delta watershed. These basin plans are the Central Valley Regional Water Board’s Water Quality Control Plan for the Sacramento and San Joaquin River basins and the San Francisco Bay Regional Water Quality Control Board’s Water Quality Control Plan for the San Francisco Bay region. For water subject to the Clean Water Act, the beneficial use designations in these two basin plans serve as designated uses under the Clean Water Act, and the water quality objectives to protect those uses serve as criteria under the Clean Water Act.
The State Water Board’s Bay-Delta Plan is a recognition that discharges of waste, including discharges regulated through National Pollution Discharge Elimination System (NPDES) permits and Waste Discharge Requirements for nonpoint source discharges, are not the only source of pollution affecting the Bay-Delta. The State Water Board is responsible for adopting and updating the Bay-Delta Plan to protect beneficial uses of water related to water diversions and operations in the Bay-Delta watershed.
Together, the Bay-Delta Plan and the two regional water board basin plans are intended to be complementary to one another and address the range of water quality and water diversion activities within the state and regional water boards implementation authorities that may impact beneficial uses of water, as well as identifying and including recommendations and actions by others to protect beneficial uses of water. The state and regional water boards are required under California law and federal law to periodically review Water Quality Control Plans and to update these plans as needed.
The first Bay-Delta Plan was developed by the State Water Board in 1978 and was subsequently updated in 1991, 1995, and 2006. The plans have generally required the State Water Project and the Central Valley Project to meet certain water quality and flow objectives in the Delta to maintain desired salinity levels for in-Delta diversions and to maintain fish and wildlife, among other things. Implementation of these objectives has often affected the amount of water available to be exported, thus at times resulting in reduced Delta exports to water users south of the Delta.
At the center of the Bay-Delta Water Quality Control Plan: setting objectives
The Bay-Delta Plan identifies beneficial uses of the Delta’s waters and then establishes water quality objectives to protect those uses. The 2006 update of the Bay Delta Plan identified 17 beneficial uses, including municipal and domestic supply, agricultural supply, groundwater recharge, navigation, recreation, fishing, wildlife habitat, and estuarine habitat.
The Bay-Delta Plan contains water quality objectives that are both narrative and numeric. Narrative objectives describe the general water quality and flow conditions that must be attained through watershed management, such as “To protect and restore the natural flow regimes of the Bay-Delta system to support the ecological functions necessary for the survival and recovery of native species.” Numeric objectives are specific numbers, for example, cubic feet per second flow or percentage of unimpaired flow.
The Bay-Delta Plan sets specific objectives for constituents, such as salinity or dissolved oxygen; inflows to the Delta from the Sacramento and San Joaquin rivers as well as for Delta outflow into the San Francisco Bay; and limits on the amount of water that is exported from the Delta.
In determining water quality and flow objectives, the Board is required by law to balance the competing uses of water to protect public trust uses, including fish and wildlife, while also considering the public interest in drinking water, hydropower, agriculture, and other beneficial uses. The State Water Board then determines how to achieve those objectives, usually by setting conditions on water rights permits or licenses or through actions such as regulation of discharges of pollutants or projects that manage agricultural drainage.
The review, development, and adoption of water quality and flow objectives require public participation, as well as consideration of alternatives and preparation of environmental documents in accordance with CEQA.
Going with the flow …
There has been a dramatic decline in populations of native fish species that migrate through and inhabit the Delta, pushing some species to the brink of extinction. While multiple stressors have contributed to the decline, the magnitude of diversions out of the Sacramento, San Joaquin, and other rivers feeding into the Bay-Delta is one of the major reasons for the ecosystem decline.
Flow influences nearly every feature of habitat that impacts fish and other wildlife, including water temperature, water chemistry, and the availability of physical habitat. These features, in turn, affect the risk of disease and predation, reproductive success, growth, migration, and feeding behavior of native fish. However, increasing flow objectives and requiring more water to remain instream reduces the surface water available for human uses, especially during drier years. The reduced water supply would primarily affect agriculture but would also affect drinking water supplies and hydropower generation.
The Delta Reform Act of 2009 directed the State Water Resources Control Board to develop new flow criteria for the Delta’s ecosystem necessary to protect public trust resources to better inform planning decisions for the Bay Delta Plan update and other State Water Board processes. In August of 2010, the State Water Board adopted the report, Final Report on the Flow Criteria for the Sacramento-San Joaquin Delta Ecosystem, which specified the volume, quality, and timing of water necessary for the Delta under different hydrologic conditions that would be needed solely for protecting fish and wildlife. It is important to note that the report did not consider competing uses of water, such as hydropower, municipal uses, and agricultural supply, and flow criteria are just one factor that the State Water Board will take into consideration when setting flow objectives, as the Board is required by law to consider and balance all the beneficial uses.
Updating the Bay Delta Water Quality Control Plan
The State Water Board is currently in the process of developing and implementing updates to the Bay Delta Plan, a project that began in 2009. In 2018, the Board adopted new flow objectives for the Lower San Joaquin River and its tributaries and revised southern Delta salinity objectives. The second phase, still in progress, will consider objectives for the Sacramento River and its tributaries, Delta eastside tributaries, Delta outflows, and interior Delta flows.
PHASE 1: San Joaquin River tributaries and Southern Delta salinity objectives
The first phase of the update considered potential changes to the San Joaquin River flow objectives to protect fish and wildlife beneficial uses in the San Joaquin River and its salmon-bearing tributaries, as well as salinity objectives to protect agricultural beneficial uses in the southern Delta.
After nine years of studies and public outreach, in December 2018, the State Water Resources Control Board adopted new flow objectives for the Lower San Joaquin River and its three tributaries, the Stanislaus, Tuolumne, and Merced Rivers. The final Lower San Joaquin River/Southern Delta update included increased instream flows from February through June, the critical months for migrating fish; the flows are measured as a percentage of “unimpaired flow,” which is defined as the amount of water moving downriver if there were no dams or other diversions. The Board also revised the salinity standard for the southern Delta, increasing slightly from prior seasonal standards.
Efforts are currently underway to develop an implementation plan for the updates and to consider a voluntary agreement on the Tuolumne River.
PHASE 2: Changes to the Sacramento River and Delta objectives
The State Water Board is currently in the process of considering updates to the portions of the Bay-Delta Plan covering the Sacramento River and the Delta. This includes the Sacramento River and its tributaries, the Delta east side tributaries, including the Cosumnes, Mokelumne, and Calaveras Rivers, and the Delta. This area is referred to as the Sacramento Delta watershed.
The State Water Board began the update in 2012. In 2017, the final scientific basis report was released, which identified the science supporting possible year-round inflows and temperature management measures for the Sacramento River, its tributaries, and Delta eastside tributaries; associated Delta outflows that would provide for required inflows in the Bay-Delta Plan to be provided as outflow; and interior Delta flows to prevent impacts to native fish from Delta water export operations.
On July 6, 2018, the State Water Board released a framework document that outlined how the State Water Board intends that each watershed in the Delta’s watershed would share in the responsibility for protecting fish and wildlife for the betterment of the entire Bay and Delta ecosystem. Key provisions described in the framework include a proposed new tributary inflow objective ranging from 45 to 65% of unimpaired flow, a new narrative cold water habitat objective, a new outflow objective for the Delta, and updated requirements governing how water circulates within the Delta. Click here to read the framework.
For all documents related to phase 2, click here.
Voluntary Agreements – A new hope?
In an effort begun by Governor Jerry Brown’s administration and continuing under Governor Gavin Newsom’s administration, the California Natural Resources Agency and the California Environmental Protection Agency have been leading an effort to negotiate voluntary agreements to improve conditions for native fish. The negotiations have been underway since at least 2018. In the early years, the negotiations included both San Joaquin Valley and Sacramento Valley water users. However, the San Joaquin Valley water users could not reach an agreement, and the process for them fell apart. The Sacramento Valley water users remain actively engaged in the process.
In September 2023, the State Water Board released the draft staff report. The draft staff report evaluates the potential benefits and environmental, economic, and other impacts and associated mitigation measures for possible alternatives for updating the Sacramento Delta portions of the Beta Delta Plan, including the proposed plan amendments and VAs. The draft staff report also assesses other standalone and modular alternatives that the State Water Board may consider.
The proposed VAs include a combination of flow and non-flow habitat restoration measures on the Sacramento, Feather, American, Yuba, and Mokelumne Rivers, and Putah Creek and in the Delta proposed by water users in the watershed.
If successful, these agreements hold the potential to help recover native fish populations more quickly and holistically than regulatory requirements and with less negative social and economic impacts; if not, litigation will surely ensue and complicate any attempts to improve conditions for years, if not a decade or more.
Reaching agreement on the voluntary agreement proposal has proven elusive. In March of 2024, the State Water Board held a three-day workshop focused on the components of the voluntary agreement proposed for the Sacramento Valley, now renamed “Healthy Rivers and Landscapes.” So far, environmental organizations have not been exactly enthused with what’s on the table for the voluntary agreements and say they were excluded from the process. So, whether the negotiations over the voluntary agreements will be successful remains very much in question.
Click here for more on the voluntary agreements.
Latest news on the Bay Delta Water Quality Control Plan
Click here for all posts on the Bay-Delta Plan from Maven’s Notebook.
