An official website of the United States government.

This is not the current EPA website. To navigate to the current EPA website, please go to This website is historical material reflecting the EPA website as it existed on January 19, 2021. This website is no longer updated and links to external websites and some internal pages may not work. More information »

San Francisco Bay Delta

Bay Delta Activities

Owl standing next to burrow in a fieldWestern Burrowing OwlThis page describes EPA actions that are focused on protecting and restoring the San Francisco Bay Delta Watershed under the Clean Water Act HelpClean Water Act Common name for the Federal Water Pollution Control Act. Its purpose is to "restore and maintain the chemical, physical and biological integrity of the nation's waters," whether on public or private land. It authorizes the U.S. Environmental Protection Agency (EPA) to set water quality criteria for states to use to establish water quality standards..

On this page:

Sacramento-San Joaquin Delta

The Bay Delta Watershed is confronted by a wide range of challenges that are magnified and concentrated in the Sacramento-San Joaquin Delta, the heart of California's water supply system. Decades of pollution and water exports have led to sharp declines in Bay Delta fisheries contributing to the collapse of native and recreational fish populations and California's salmon fishing industry. Droughts and declining fish populations have forced water supply reductions for agriculture and cities. EPA is focused on the Delta and working with federal and State partners to restore aquatic life protection and secure a reliable water supply for agriculture, industry, and municipal uses.

San Francisco Bay Delta Action Plan

EPA is advancing seven priority actions to restore protection to aquatic life in the Bay Delta Estuary. These steps are identified in our San Francisco Bay/Sacramento-San Joaquin Delta Action Plan (August 2012) and were informed, in part, by a review of aquatic life protection by CWA programs and public comments that were triggered by an Advance Notice of Proposed Rulemaking for Water Quality Challenges in the SF Bay Delta Estuary.

Technical Support

EPA provides technical support and regulatory assistance for priority activities designed to improve water supply reliability and aquatic life protection in the Delta.

Navigation, Dredging, and Sediment Management

Dredging is necessary to create and maintain navigation channels to our nation's ports, harbors, marinas, and naval facilities but it can also negatively impact aquatic ecosystems. EPA is focused on increasing beneficial reuse of dredged material as one of the primary goals of long term sediment and dredging management strategies.

EPA Region 9 Dredging and Sediment Management Program activities in the San Francisco Bay Delta Watershed include managing the San Francisco Deep Ocean Disposal Site and the San Francisco Bar Disposal Site, co-chairing the San Francisco Bay Long Term Management Strategy, and participating in developing the Delta Long Term Management Strategy.

Top of Page

San Francisco Bay

San Francisco Bay Water Quality Improvement Fund

EPA directs the San Francisco Bay Water Quality Improvement Fund, a competitive grant program that provides funding for projects to protect and restore San Francisco Bay and its watershed. EPA is funding 49 grants, involving over 80 partners to achieve significant environmental improvements related to wetlands, water quality and green development.

Congress has appropriated over $58 million in funding since 2008 to the San Francisco Bay Water Quality Improvement Fund. EPA has worked with state and federal partners who are contributing an additional $168 million to restore wetlands and watersheds, and reduce polluted runoff.

EPA also works with the San Francisco Bay Water Quality Control Board and local partners on the Regional Monitoring Program for Water Quality in San Francisco Bay, administered by the San Francisco Bay Estuary Institute, which monitors contamination in the San Francisco Bay and publishes an annual Pulse of the Bay report.

National Estuary Program

The San Francisco Estuary Partnership (SFEP) provides public education and manages research and habitat restoration projects for the protection of San Francisco Estuary aquatic resources. SFEP was established in 1987 under the Clean Water Act National Estuary Program. There are 28 EPA designated National Estuary Programs. The purpose of each program is to collaboratively develop and implement an EPA-approved Comprehensive Conservation and Management Plan (CCMP). The SFEP CCMP geographic scope includes 60,000 acres of watershed drainage to the San Francisco Bay and Delta. SFEP recently developed a strategic plan to direct resources to wetland and watershed restoration, water quality improvements through green infrastructure, and climate change readiness, with most activities focused on the nine San Francisco Bay Area counties. EPA provides annual funding to SFEP.

Top of Page

Central Valley

EPA advances water quality improvement in the Central Valley by supporting many activities such as river restoration, regional monitoring, adoption and implementation of water quality improvement plans (TMDLS), and working with water quality partners such as NRCS to leverage water quality improvement investments. Links to more information about EPA's role in some of these investments are listed below.

  • San Joaquin River Restoration Program
  • EPA funded the Proposed Strategy for San Joaquin River Basin Water Quality Monitoring and Assessment
  • Strawman Proposal for San Joaquin Valley Regional Monitoring (PDF) was developed in 2012 by the Coalition for Urban/Rural Environmental Stewardship, EPA and the California Water Resources Board.
  • EPA supported the development of the Central Valley Watershed Monitoring Directory which is intended to improve coordination of water monitoring across the basin.

Top of Page