Bay-Delta Water Quality and Water Rights Advocacy

About the Case

California’s San Francisco Bay/Sacramento-San Joaquin Delta (“Bay-Delta”) is a vast watershed encompassing the largest estuary on the west coast of North and South America and the world’s only inland delta. Nearly half the surface water in California starts as rain or snow in the watershed, draining into two major rivers—the Sacramento River to the north and the San Joaquin River to the south—that converge to form the Delta. Unimpaired, water flows through the Delta into the Suisun Marsh and on into the San Francisco Bay. Sufficient freshwater flows are needed to maintain the Delta’s diverse fish and wildlife habitat and support native riparian species, to flush nutrients and sediments, and to keep the salinity mixing zone from extending further inland, disrupting native fish habitat and compromising water supplies.

Native American Tribes have called the Delta home since time immemorial and continue to center cultural and spiritual traditions on its rivers and the life they sustain. The Delta is also home to diverse rural and urban communities who rely on freshwater flows for drinking water, recreation, and an array of environmental services.

Demand for freshwater throughout the state has dramatically altered the Delta landscape and the relationship Delta Tribes and communities hold its with its waterways. The State Water Project (operated by the California Department of Water Resources, or “DWR”) and federal Central Valley Project (operated by the U.S. Bureau of Reclamation) together comprise a coordinated network of dams, aqueducts, and pumping stations that store and export vast amounts of Delta water for agricultural and municipal use in other parts of the state. Water exports combined with upstream diversions have reduced annual average Delta outflows by nearly half (from 28.5 million acre-feet to 15.5 million acre-feet per year) and by as much as 80 percent in dry years. Current regulatory outflow controls require only about five million acre-feet per year, less than 20 percent of unimpaired flows. Heavy reliance on Bay-Delta flows combined with inadequate water quality controls have driven the Bay-Delta ecosystem into a widely recognized state of crisis. Climate change is exacerbating ecosystem impacts while proposals for new storage and conveyance facilities and projected population growth add new pressures on Delta flows.

In 2021, a coalition of California Native American Tribes, whose ancestral homelands span the Delta and its headwaters, came together with environmental justice organizations in the urban Delta to press for restoration of instream flows in the Bay-Delta, protection of cultural and subsistence uses of waterways, and a healthier future for the imperiled Delta ecosystem and communities reliant on its freshwater flows. The Delta Tribal Environmental Coalition, or “DTEC,” includes the Shingle Springs Band of Miwok Indians, Winnemem Wintu Tribe, Little Manila Rising, and Restore the Delta. The Clinic is counsel for DTEC on various proceedings, including the Delta Conveyance Project water rights adjudication and efforts to update instream flows standards and protect Tribal Beneficial Uses of Delta waters.

Delta Conveyance Project Water Rights Adjudication

In 1972, the California State Water Resources Control Board (State Water Board) which administers water rights in the state, issued four water permits to the California Department of Water Resources (DWR) authorizing the agency to divert up to 10,350 cubic feet per second of water from the Feather River and Delta channels to operate the State Water Project. The permits originally required DWR to complete construction of diversion projects by December 1980 and apply water allotted under the permits to full beneficial use by December 1990. On application by DWR, the State Water Board extended the construction timeline to December 2000 and the deadline to put the water to the proposed use to December 2009. On December 31, 2009, DWR applied for a further five-year extension. The State Water Project never acted on the extension request.

In February 2024, DWR filed a petition with the State Water Board to modify its water rights permits for the State Water Project to construct and operate an expansive new water conveyance system—the Delta Conveyance Project. The Delta Conveyance Project would construct a 45-mile-long underground tunnel stretching from intakes points on the Sacramento River near the town of Hood to pumping stations in the south Delta, where Sacramento River water would be exported to the California Aqueduct for distribution to farms and cities. The Delta Conveyance Project would have the capacity to capture 6,000 cubic feet of water per second.

On May 13, 2024, DTEC, represented by the Clinic, filed a protest to the water rights petition along with the San Francisco Baykeeper, California Indian Environmental Alliance, Golden State Salmon, Association, Pacific Coast Federation of Fishermen’s Associations, and Institute for Fisheries Resources. The petition and protests were assigned to the State Water Board Administrative Hearings Office for formal adjudication.

Evidentiary proceedings began in spring 2025, with direct examination of DWR case-in-chief witnesses and cross-examination by Clinic student attorneys and other parties. On July 11, 2025, the Clinic submitted written case-in-chief testimony by eight witnesses on behalf of DTEC focusing on the Delta Conveyance Project’s impacts on Tribal lands, resources, and beneficial uses of water; its impacts on proliferation of harmful algal blooms; and demographic disparities in the location of the Project’s construction sites. Examination of protestants’ case-in-chief witnesses as well as site visits of the Project area concluded in December 2025. Evidentiary proceedings will continue in spring 2026 with rebuttal testimony.

Instream Flow Standards and Tribal Beneficial Use Protections in the California Bay-Delta

In May 2022, DTEC filed a petition for rulemaking with the California State Water Resources Control Board to update water quality standards for the Bay-Delta. The federal Clean Water Act, 23 U.S.C. § 1313, requires states to adopt water quality standards for waterways within their jurisdiction, comprising designated uses and numeric or narrative criteria to protect those uses. Water quality standards must be reviewed with public hearings every three years and updated as necessary to protect beneficial uses. The water quality standards for the Bay-Delta were last comprehensively updated in 1995, and the State Water Board has recognized that current Delta outflow requirements are “too low to protect the ecosystem.”

The petition called on the State Water Board to update Bay-Delta water quality standards through a public process informed by government-to-government consultation with Tribal Nations; to designate Tribal cultural and subsistence water uses for formal protection; and to adopt numeric criteria to control harmful algal blooms. Toxin-producing harmful algal blooms have emerged in Delta rivers in recent years as a result of low flows combined with high nutrient loads and warming temperatures, posing risks to community and ecosystem health and disrupting recreation and cultural practices.

After the State Water Board denied the petition, the Coalition called on the U.S. Environmental Protection Agency (EPA) to intervene. In December 2022, DTEC and Save California Salmon filed a civil rights complaint with EPA against the State Water Board, alleging that the Board’s failure to update water quality standards discriminates against Delta Tribes and communities of color. In August 2023, EPA accepted the Title VI Complaint and opened an investigation into civil rights violations by the State Water Board. The parties agreed to seek an informal resolution of the complaint through a facilitated negotiation process. EPA’s investigation into civil rights violations by the State Water Board remains pending.

Meanwhile, the State Water Board moved forward with an update to the Bay-Delta water quality standards. In fall 2023, the Board released a staff report and environmental review document, followed by a proposed update to the Bay-Delta water quality control plan in October 2024. The clinic, on behalf of DTEC, filed written comments on the proposed update on January 10, 2025. DTEC’s comments laud the Board for its proposal to integrate Tribal Cultural Use designations into Bay-Delta water quality standards while taking issue with the Board’s proposal to substitute negotiated commitments by water rights holders (referred to in the plan as Voluntary Agreements) for regulatory minimum instream flow standards and for declining to adopt water quality criteria for control of harmful algal blooms, as well as its refusal to undertake formal government-to-government consultation with Tribes on the proposed update.

The Board issued a revised water quality control plan and initiated a limited recirculation of the environmental review document on December 12, 2025 for further public comment. Hearings on the proposed update are scheduled for February 2026.