San Francisco Bay: A Freshwater Starved Estuary

Bay Institute | September 1st, 2016

How Reducing Flows Harms the Ecosystems of San Francisco Bay and Coastal Waters The Bay Institute’s major new study, San Francisco Bay: The Freshwater – Starved Estu

How Reducing Flows Harms the Ecosystems of San Francisco Bay and Coastal Waters The Bay Institute’s major new study, San Francisco Bay: The Freshwater – Starved Estuary, documents how the ecological health of San Francisco Bay and the nearby ocean is at high risk because large-scale water diversion in the Bay’s watershed severely limits the amount of fresh water that reaches the Bay and alters the timing of that flow. Inflow to the Bay from its Central Valley watershed now averages less than half of what it would be without diversions; in some years just one-third of the runoff makes it to the Bay. The result is a nearly permanent drought for the Bay’s fish, wildlife, and their habitats. This radical alteration creates severe consequences for the Bay and marine ecosystems – and Bay Area residents pay the price. The study shows how unsustainable diversion of the Bay’s freshwater inflow: Dramatically cuts production of fish and shrimp that are the food source for marine mammals, like Orca Whales, and birds; Allows pollutants to accumulate to dangerous levels and encourages blooms of toxic algae; Reduces sediment supply to Bay Area wetlands and beaches; Makes it easier for undesirable non-native species to successfully invade the Bay Estuary. The San Francisco Bay Estuary is created by the mixing of fresh water from the Central Valley’s rivers with salt water from the Pacific Ocean. Dramatically reducing the inflow of fresh water generates cascading effects in the Bay’s watershed, the Bay itself, and coastal ocean waters. The report’s major findings include: On average, since 1975 more than half (53%) of runoff from the Central Valley watershed has been diverted, stored, or exported before it can reach the Bay – and in many years two-thirds or more of the Bay’s inflow is captured; As a result of intensive water diversions, the Bay experiences catastrophically dry years almost half the time (only one “supercritically dry” year occurred naturally between 1975-2014, but the Bay experienced nineteen supercritical years during that period); Numerous unrelated fish species – from sharks to salmon, from sturgeon to smelt – show strong positive correlations with Bay Inflow; many of these species are now endangered, and even commercially viable fisheries are in decline; Predators that feed on flow-dependent fish and shrimp are feeling the pinch – for example, dwindling supplies of Central Valley Chinook salmon may restrict the recovery of the local Orca whale population; Blooms of toxic “algae” (cyanobacteria) are becoming more frequent, and other pollutants are becoming more concentrated, as a result of reductions in freshwater flows from the Bay’s watershed; Bay Area beaches and tidal wetlands are deprived of sediment that was once transported by high river flows. The study reports that local businesses are likely to suffer from the Bay’s continued decline, including those related to commercial fishing and tourism. As our Bay, beaches, wetlands, and fish and wildlife populations deteriorate, the quality of life for many Bay Area residents will also be severely – and perhaps permanently – damaged. The study identifies four important approaches to improving Bay inflows: Update the State’s 21 year old water quality standards for the Bay Estuary to ensure adequate inflow Require all those who divert water destined for the Bay, not just a subset, to contribute their fair share of fresh water to support benefits enjoyed by all Californians Invest in local water supplies around the state including conservation, and recycling, that can generate millions of acre-feet of water and reduce reliance on water diverted from the Estuary and its watershed Coordinate management of flows with wetland and beach restoration to more effectively protect shorelines The study was prepared for the San Francisco Estuary Partnership, a coalition of resource agencies, non-profits, citizens, and scientists working to protect, restore, and enhance water quality and fish and wildlife habitat in and around the San Francisco Bay Delta Estuary, which also provided the majority of funding for the project.

San Francisco Estuary Blueprint 2022

San Francisco Estuary Partnership (SFEP) | September 8th, 2022

In the past few years, the San Francisco Estuary region has confronted epic wildfires, historic rainfall intensity and flooding, and chronic drought. The whiplash of thes

In the past few years, the San Francisco Estuary region has confronted epic wildfires, historic rainfall intensity and flooding, and chronic drought. The whiplash of these events has confirmed that climate change has already begun to impact human and wildlife communities from Sacramento to San Francisco, and beyond. Furthermore, a global COVID-19 pandemic has disrupted regional planning and project implementation everywhere, presenting new challenges to traditional processes and creating an unfamiliar working landscape for resource managers. Finally, the pervasive, horrific violence against Black, Brown, and Asian and Asian-American people has amplified long-term calls for racial justice, galvanizing new commitments to address historic and present inequity through every thread of our social fabric. These events have set the context for the multi-stakeholder process that updates the San Francisco Estuary Blueprint.

San Francisco Estuary Blueprint 2022 (Comprehensive Conservation and Management Plan for the San Francisco Estuary)

San Francisco Estuary Partnership (SFEP) | March 16th, 2022

Click here for the definition of a Comprehensive Conservation and Management Plan)

Click here for the definition of a Comprehensive Conservation and Management Plan)

San Joaquin River Flow and Southern Delta Salinity Technical Report

California State Water Resources Control Board (SWRCB) | October 10th, 2011

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wild

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wildlife beneficial uses, water quality objectives for the protection of southern delta agricultural beneficial uses, and the program of implementation for those objectives contained in the 2006 Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (2006 Bay-Delta Plan). The information and analytical tools described in this report (referred to hereafter as Draft Technical Report or Technical Report) are intended to provide the State Water Board with the scientific information and tools needed to consider potential changes to these objectives and the program of implementation. In this quasi-legislative process, State Water Board staff will propose amendments to the SJR flow and southern Delta salinity objectives and program of implementation contained in the 2006 Bay-Delta Plan, and will comply with the California Environmental Quality Act including preparation of a Substitute Environmental Document (SED). The proposed amendments will include revisions to these objectives for the reasonable protection of fish and wildlife, agriculture, and municipal and industrial beneficial uses, and a program of implementation. Any changes to water rights consistent with the revised program of implementation will be considered in a subsequent adjudicative proceeding.

San Joaquin River Restoration Program

San Joaquin River Restoration Program | December 13th, 2007

San Joaquin Valley Conveyance Study

California Department of Water Resources (DWR) | November 24th, 2025

This San Joaquin Valley Conveyance Study analyzes water conveyance needs in the San Joaquin Valley (Figure ES-1). The purpose of this study is to: •Describe the impa

This San Joaquin Valley Conveyance Study analyzes water conveyance needs in the San Joaquin Valley (Figure ES-1). The purpose of this study is to: •Describe the impacts of subsidence on San Joaquin Valley conveyance facilities. •Evaluate the need for improved or expanded conveyance facilities throughout the San Joaquin Valley.  

San Leandro Bay PCB Study Data Report

San Francisco Estuary Institute (SFEI) | December 1st, 2017

The goal of RMP PCB special studies over the next few years is to inform the review and possible revision of the PCB TMDL and the reissuance of the Municipal Regional P

The goal of RMP PCB special studies over the next few years is to inform the review and possible revision of the PCB TMDL and the reissuance of the Municipal Regional Permit for Stormwater, both of which are tentatively scheduled to occur in 2020. Conceptual model development for a set of four representative priority margin units will provide a foundation for establishing an effective and efficient monitoring plan to track responses to load reductions, and will also help guide planning of management actions. The Emeryville Crescent was the first PMU to be studied in 2015-2016. The San Leandro Bay PMU is second (2016-2017), Steinberger Slough in San Carlos is third (2017), and Richmond Harbor will be fourth (2018). The conceptual model reports for these four PMUs will be developed and presented using a consistent framework, and will build on each other to form an integrated assessment of these four areas. The lessons learned from these analyses will also be more generally applicable to similar contaminated sites on the margins of the Bay. This document is a data report on field studies to support development of a conceptual model for San Leandro Bay.

San Luis National Wildlife Refuge Complex Final Comprehensive Conservation Plan and Environmental Assessment

U.S. Fish and Wildlife Service (FWS) | July 31st, 2024

This Comprehensive Conservation Plan (CCP) will guide the management of the Merced National Wildlife Refuge (NWR), San Luis NWR and Grasslands Wildlife Management Area (W

This Comprehensive Conservation Plan (CCP) will guide the management of the Merced National Wildlife Refuge (NWR), San Luis NWR and Grasslands Wildlife Management Area (WMA) for the next 15 years. Located in Merced County, California (Figure 1-1), these three units are managed and administered by the San Luis National Wildlife Refuge Complex (the Complex). A fourth unit, the San Joaquin River NWR, is also managed and administered by the Complex but already has a CCP for its management, which was completed in 2006 and amended in 2022. For the sake of this document, the term Complex refers to the San Luis NWR, Merced NWR and Grasslands WMA only. The Complex comprises just four of the 568 refuges that currently make up the U.S. Fish and Wildlife Service (USFWS or the Service) National Wildlife Refuge System (NWRS or Refuge System). The mission of the NWRS is to conserve a network of lands and water for the conservation and management of fish, wildlife and plant resources of the United States for the benefit of present and future generations. As part of the Refuge System, the three units—Merced NWR, San Luis NWR and Grasslands WMA—addressed in this CCP provide important habitat for a unique assemblage of both wetland- (particularly waterfowl and other waterbirds) and upland-dependent wildlife species of California’s Central Valley. This CCP is divided into five chapters: Chapter 1, Introduction and Background; Chapter 2, Comprehensive Conservation Planning Process; Chapter 3, Refuge Resources; Chapter 4, Refuge Management Direction; and Chapter 5, Implementation. Click here for full appendices.

Sand Supply to San Francisco Bay from the Sacramento and San Joaquin Rivers of the Central Valley, California

U.S. Geological Survey (USGS) | October 30th, 2024

Sediment from the Central Valley via the Sacramento-San Joaquin Delta (Delta) and Suisun Bay is a primary source of sand to San Francisco Bay, California. Sand is mined f

Sediment from the Central Valley via the Sacramento-San Joaquin Delta (Delta) and Suisun Bay is a primary source of sand to San Francisco Bay, California. Sand is mined from San Francisco Bay for commercial purposes, such as for use in concrete for construction. To better understand the supply of sand to Suisun Bay and San Francisco Bay, the U.S. Geological Survey (USGS), in cooperation with the San Francisco Bay Estuary Institute (SFEI) and the San Francisco Bay Conservation Development Commission (BCDC), initiated this study to compile and synthesize historical data and estimate the total sediment and sand portion of sediment exiting the Delta to Suisun Bay for a 20-year period between water years 2001 and 2020.

Scientific Basis Report in Support of New and Modified Requirements for Inflows from the Sacramento River and its Tributaries and Eastside Tributaries to the Delta, Delta Outflows, Cold Water Habitat, and Interior Delta Flows

California State Water Resources Control Board (SWRCB) | October 2nd, 2017

The State Water Board is conducting a review and update of the 2006 Bay-Delta Plan to ensure that beneficial uses of water in the Bay-Delta watershed are reasonably prote

The State Water Board is conducting a review and update of the 2006 Bay-Delta Plan to ensure that beneficial uses of water in the Bay-Delta watershed are reasonably protected. Phase I addresses potential changes to San Joaquin River flow requirements for the protection of fish and wildlife and potential changes to southern Delta salinity requirements for the protection of agriculture.1 Phase II addresses changes to the Bay-Delta Plan to protect native fish and wildlife in the Sacramento River, Delta, and associated tributaries. This Scientific Basis Report (Science Report or Report) is being prepared to support the Phase II update of the Bay-Delta Plan. It describes the science on which proposed changes to the Bay-Delta Plan will be based. A working draft version of the Report was released on October 19, 2016, to receive early scientific and public input on the science related to Phase II prior to submittal of the Report for external peer review. The State Water Board received input from a number of interested parties including water users; environmental groups; and local, state, and federal agencies. In recognition of the vision for “one Delta, one science” articulated in the Delta Stewardship Council’s (DSC) Delta Plan, the State Water Board also requested that the Delta Independent Science Board (Delta ISB) conduct a review of the Report. The State Water Board appreciates the valuable comments and suggestions that have helped further strengthen the scientific content in this version of the Report. In addition, comments related to regulatory and policy issues were raised that have further informed the development of proposed changes to the Bay-Delta Plan, including implementation approaches. The general components of these changes are summarized below and in more detail in Chapter 5 for context, and will continue to be refined as the planning process moves forward. This Report and the peer reviewers’ responses will be posted on the State Water Board web site and become part of the record for this Bay-Delta Plan update. Content from this Report will be included in a larger Staff Report that will also contain information on environmental, economic, and other analyses of potential changes to the Bay-Delta Plan, including regulatory and policy considerations of competing uses of water (including municipal, industrial, agricultural, power production, and other environmental uses of water such as wetland and wildlife refuge supplies). These issues are not addressed in this Science Report. Further, while a description of the approach for proposed changes to the Bay-Delta Plan is provided, the exact regulatory language is still under development and will be informed by the science in this Report and other information that will be included in the Staff Report. The public and agencies will continue to have opportunities to provide input throughout this process.