Bay Delta Water Quality Control Plan (Bay Delta Plan)


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.

This page last updated on July 6, 2018.

The Bay Delta Plan was last updated in 2006. Click on the document to read.

The Sacramento-San Joaquin Delta watershed covers more than 75,000 square miles, extending nearly 500 miles from the Cascade Range in the north to the Tehachapi Mountains in the south, bounded by the Sierra Nevada Mountains to the east and the Coast Range to the west. Nearly half of the water flowing in the state’s rivers and streams starts as rain or snow that falls within the watershed and flows downstream through the Delta.  The Delta watershed is home to the largest estuary on the west coasts of the Americas, as well as the primary source of drinking water for 25 million Californians and irrigation for millions of acres of farmland.

In recent years, declining water quality, plummeting populations of native fish, and increasing demand for limited water resources have been at the heart of several state agency planning processes, one of those being the State Water Resources Control Board’s Bay-Delta Plan.

The ‘San Francisco Bay/Sacramento-San Joaquin Delta Estuary Water Quality Control Plan,’ blessedly known as ‘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. Usually water quality control planning is generally done by the regional water boards; however, the State Water Board develops and adopts the Bay Delta Plan due to the importance of the Delta as a major source of water supply for the state.

The Bay Delta Plan is implemented through Water Right Decision 1641. Click on the document to read.

The State Water Board is a bit behind in the updating process.  Under the Clean Water Act, water quality control plans are to be updated every three years; however the Bay Delta Plan has been updated and revised only three times in the last 38 years with the last full review taking place in 1995; those standards were finally implemented into water rights permits in 2000 with Decision 1641.  The existing Bay-Delta Plan was adopted in 2006.  The current update began in 2009 and is not expected to be completed before 2018 – at the earliest.

This update of the Bay-Delta Plan is focusing on evaluating the impact of insufficient freshwater flows as numerous scientific documents have identified flow as a major factor affecting fisheries and other public trust uses of the waters of the Delta.  Given that the State Water Board stated in a 2010 report, (pg. 15) “the best available science suggests that current flows are insufficient to protect public trust resources,” it is widely expected that the water board will adopt flow objectives that will require increased freshwater flows through the Delta.


The Bay-Delta Plan identifies beneficial uses of the Delta’s waters and then establishes Delta Babel Slough #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.  (For a complete list of the Delta's beneficial uses, click here.)

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 right permits or licenses, or through actions such as regulation of discharges of pollutants or projects that manage agricultural drainage.

Stocktonians enjoying the Delta on a summer eveningThe 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.

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.

Delta Afternoon July 2015 #12 sliderbox


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 in order to better inform planning decisions for the Delta Plan and the Bay Delta Conservation Plan (now California Water Fix), as well as the State Water Board’s 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 specifies the volume, quality, and timing of water necessary for the Delta under different hydrologic conditions to protect fish and wildlife.  The report did not consider competing uses of water, such as hydropower, municipal uses, and agricultural supply.

Bird in the brush at Three Mile Slough #2 04-2008 smallerFelicia Marcus explained the reason behind the development of the flow criteria in her speech at the UC Davis California Water Policy Seminar Series: “It basically was if the fish could talk, what would the fish ask for, and was a counterpoint to what the water suppliers had been asking for, so that as we moved into this planning process, both at the BDCP and the water board, that the fishes voice would be thrown into mix rather than ignored.”

Flow criteria is just one factor that the State Water Board will take into consideration when setting flow objectives as they are required by law to consider and balance all the beneficial uses, which include not only the protection of fish and wildlife, but also all of the Delta's other beneficial uses, such as municipal and agricultural water use, hydropower, and recreational uses.  Given how contentious water issues can be, this balancing of competing uses generally means that if the State Water Board had done a good job of it, no one stakeholder group is going to be completely satisfied.

  • Read the report, Final Report on Development of Flow Criteria for the Sacramento-San Joaquin Delta Ecosystem, by clicking here.

An egret and ring-billed gulls congregate on Staten Island on December 14, 2013.


The State Water Board is currently in the process of developing and implementing updates to the Bay Delta Plan in four distinct phases.

PHASE 1: San Joaquin River tributaries and Southern Delta salinity objectives

San Joaquin River July 2013 #4

The first phase of the update considers potential changes to the San Joaquin River flow objectives in order 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.

In December of 2012, the State Water Board released a draft Supplemental Environmental Document (SED); in September of 2016, the Board released revised SED which incorporated changes in consideration of the large number of comments received, new information, and the passage of the Sustainable Groundwater Management Act.  The public comment on the second draft of the Phase 1 SED closed on March 17, 2017.

The proposal for phase 1 objectives would increase the amount of required flows to be left in the Stanislaus, Tuolumne, and Merced Rivers; the water would be provided as a block of water that could be adaptively managed to benefit species. The proposal would also eliminate the seasonal objectives for salinity standards in the south Delta in effect raising the salinity levels during certain times of the year.

On July 6, 2018, the State Water Resources Control Board released the draft final documents for the San Joaquin River tributaries and southern Delta salinity objectives.  The State Water Board will consider adopting the Proposed Final Amendments and Final SED at a pubic meeting on August 21, 2018. The State Water Board will accept written comments on the Final SED until 12:00 p.m. noon on July 27, 2018.

To access all the documents for the lower San Joaquin River and Southern Delta salinity objectives, click here.

PHASE 2: Changes to the Sacramento River and Delta objectives

The second phase focuses on the other parts of the Bay-Delta Plan not covered in Phase one and will include new inflow requirements for the Sacramento River, its tributaries, and eastside tributaries to the Delta (the Mokelumne, Calaveras and Cosumnes rivers); new and modified Delta outflow requirements; new requirements for cold water habitat; new and modified interior Delta flow requirements; recommendations for complementary ecosystem protection actions that others should take; and adaptive management, monitoring, evaluation, special study, and reporting provisions.

Sacramento River in the Delta, picture by US FWSOther potential changes to be considered during this phase include issues identified through the scoping process, and information that is produced as part of the California Water Fix (formerly the Bay Delta Conservation Plan).

On July 6, 2018, the State Water Board released a framework document for the update for the Sacramento River and the Delta at the same time the documents for phase 1, the San Joaquin River and Southern Delta salinity objectives to allow the public to better understand how the two updates relate to one another and 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 that ranges 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 itself.  Click here to read the framework.

A detailed staff report is expected later in 2018 and will  include analyses of different environmental benefits and water supply costs, an analysis of economic impacts, and a more detailed alternatives analysis. 

To visit the State Water Board's webpage on Phase 2, click here.

PHASE 3: Implementation

The third phase, implementation, will include determining the changes to water rights and other measures needed to implement the plan, and will begin once final objectives for phase 1 and/or phase 2 have been adopted.

PHASE 4: Development of flow objectives for high-priority tributaries to the DeltaMap of Delta tributaries, from the State Water Board

Phase four of the update process involves developing flow objectives and implementation plans for high-priority tributaries to the Delta that currently are not specifically regulated in this way.    The process will begin by first determining the flow criteria for the protection of fish and aquatic life with an emphasis on protection of threatened or endangered species; this criteria will be then taken into consideration as the objectives are tailored to each tributary to address it’s unique characteristics, public trust resources, and beneficial uses.

The State Water Board intends to develop flow criteria, flow objectives, and associated implementation plans for a minimum of five priority tributaries in the Bay-Delta watershed by 2025 and for the remaining priority tributaries thereafter.

To visit the State Water Board's webpage on Phase 4, click here.

Delta with Sacramento water tower in distance sliderbox


Click here for all posts on the Bay-Delta Plan from Maven’s Notebook.

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