San Francisco Bay Delta

EPA’s Role in Protecting the Watershed

Protecting San Francisco Bay Delta Watershed water quality through enforcement of the Clean Water Act will benefit local wildlife like this pair of Sandhill Cranes shown flying in formation
Sandhill Cranes

Under the Clean Water Act (CWA), EPA is charged with protecting and restoring the nation’s waterways, including waters in the San Francisco Bay Delta Watershed. In California, most of the Clean Water Act programs have been delegated by EPA to the State, with EPA taking an oversight role, and in some cases, a mandatory review and approval role of California’s water quality programs and policies. EPA's oversight role applies to delegated programs such as Water Quality Standards, Monitoring and Assessment, TMDLs, and NPDES programs.

EPA is directly responsible for Clean Water Act grant programs and Clean Water Act enforcement, and shares responsibility for administering the Clean Water Act Wetlands Regulatory Program with the United States Army Corps of Engineers.

Some water quality issues are addressed by the CWA in combination with other federal environmental laws that EPA and California administer. For example, mercury from coal fired power plants can be controlled by adjusting permits required under the federal Clean Air Act.

Similarly, mercury from abandoned mines is addressed by cleanup plans and removal actions pursuant to EPA’s Superfund Program. Aquatic toxicity caused by pesticides is controlled by CWA programs and EPA’s pesticide registration program under the Federal Insecticide, Rodenticide and Fungicide Act. Both the CWA and the Marine Protection, Research and Sanctuaries Act also protect water quality by establishing designated open-water disposal sites for clean material dredged out of ship channels, harbors, marinas and other areas.

EPA and Major Clean Water Act Programs

Throughout the watershed, EPA uses a variety of regulatory and other tools to protect environmental quality and conserve water and habitat. These include helping California develop watershed plans and limit total discharge loads, monitoring streams to make sure that standards are met, ensuring that dredge and fill permits comply with the Clean Water Act, and helping reduce water pollution.

  • Water Quality Monitoring and Assessment
    blue heron rising from the ground
    Blue Heron

    EPA provides financial and technical assistance to the states to monitor water quality, identify water pollution problems, and develop pollution control plans. Water quality monitoring is essential for ensuring that water quality standards are protecting a broad range of water uses. Learn more about monitoring and assessment in EPA Region 9 here.

  • Total Maximum Daily Loads (TMDLs)

    Total Maximum Daily Loads (TMDLs)

    EPA provides technical, financial and regulatory assistance for the development and implementation of TMDLs. Monitoring data and CWA Assessments show that many waterways in the San Francisco Bay Delta Watershed do not meet water quality standards. Total maximum Daily Loads (TMDLs) are pollution control plans that identify methods for attaining water quality standards. There are twenty-seven approved TMDLs in San Francisco Bay Delta Watershed and fifteen more under development.

    EPA is focused on successful TMDL development and implementation in the San Francisco Bay Delta Watershed. TMDL implementation refers to completing required TMDL actions, achieving load limits, and removing water quality impairments. Our goals include improving accountability through public tracking and accounting of TMDL progress and aligning grant and program activities to ensure timely achievement of load limits and removal of impairments.

  • Nonpoint Source Pollution

    EPA provides funding to California for their Nonpoint Source Pollution Control Program. Nonpoint source pollution - pollution caused by a wide range of activities including urban development, agriculture and forestry - is a major cause of water quality impairment nationally and in the Bay Delta Estuary watershed. The interactive map Exit EPA Disclaimer on this website shows the location of nonpoint source pollution control projects and provides a description of the activities that are reducing pollutant loadings to waterways in the San Francisco Bay Delta watershed.

  • National Pollutant Discharge Elimination System (NPDES)

    The CWA requires EPA, or delegated states like California, to control point source discharges of water pollution by issuing NPDES permits. Point sources refer direct discharges of pollutants to waterways (for example sewage treatment plants). EPA Region 9 reviews NPDES permits before they are issued by California. Point sources that are particularly relevant in the San Francisco Bay Delta Watershed are discharges from sewage treatment facilities, refineries and municipal stormwater systems. EPA also conducts inspections and takes enforcement actions as necessary to ensure that waterways are protected and permit requirements are met.

  • Wetlands

    The Clean Water Act Section 404 Program is a significant component of the Clean Water Act regulatory framework in the San Francisco Bay Delta Watershed. The goal of this program is to minimize destruction of wetlands and waterways which in turn protects water quality, provides habitat for fish and wildlife, buffers floods and erosion, and enhances ground water recharge.

    More than 90% of California's wetlands and riparian areas have been destroyed. Many of the remaining wetland areas, estuarine habitat, and streams in the Bay Delta Watershed are threatened by urban expansion and infrastructure projects.

    Section 404 of the Clean Water Act requires a permit from the US Army Corps of Engineers for dredging or filling of any waters of the United States, including wetlands. EPA works with the Corps to minimize impacts to wetlands and waterways that occur from permitted actions and ensures that the functions and values of any wetlands and waters destroyed are replaced.


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