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 Francisquito Creek Baylands Landscape Change Metrics Analysis

San Francisco Estuary Institute (SFEI) | June 21st, 2016

The goal of this study is to develop a high level overview of the physical and ecological changes to lower San Francisquito Creek and the surrounding tidal marshes and mu

The goal of this study is to develop a high level overview of the physical and ecological changes to lower San Francisquito Creek and the surrounding tidal marshes and mudflats (referred to here as “baylands”) since the beginning of intensive European-American settlement. Building upon a previous reconnaissance-level historical ecology study (Hermstad et al. 2009), this study analyzes the changes in key landscape features (or landscape metrics) within lower San Francisquito Creek and baylands through comparisons of reconstructed historical (mid-1800s) and contemporary (2011/2012) conditions. The results from this study are intended to provide baseline information that can be used to help with developing restoration and flood control redesign alternatives and appropriate habitat restoration targets. This study is one component of the Flood Control 2.0 project, a regional effort funded by the U.S. EPA to help design flood control channels at the Bay interface that support tidal habitats while maintaining the required level of flood protection. Emerging strategies for flood protection focus on reconnecting channels to floodplains and tidal marshes and using available dredged sediment as a resource to increase marsh elevations and help keep pace with sea level rise. Lower San Francisquito Creek is one of three implementation projects that have partnered with Flood Control 2.0 to assess the benefits of an integrated approach for flood control and habitat management at the Bay interface.

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.

Seasonality of Retreat Rate of a Wave-Exposed Marsh Edge

American Geophysical Union (AGU) | July 10th, 2024

Waves can cause destruction of marshlands when they collide with the boundary of the marsh area. We studied how the speed of marsh loss from waves can change between seas

Waves can cause destruction of marshlands when they collide with the boundary of the marsh area. We studied how the speed of marsh loss from waves can change between seasons with different climates. To do this we made five 3D models of a marsh in South San Francisco Bay over a single year and looked at their differences between summer/fall/winter/spring. We found fast marsh loss in the seasons where daily winds are common (spring/summer), and minor changes in seasons with storms but without daily winds (fall/winter). Across our entire marsh, we saw lots of variety in how much it was changing, including some addition (i.e., positive change) to the mudflats near the marsh in the fall/winter. When we compared the marsh loss over one year to what was lost between 2004 and 2019, the speeds were similar, so we believe our study period was similar to long‐term marsh dynamics. This work encourages incorporating different seasonal climates into expectations of how marshes evolve, and supports that we need to think about marshes and mudflats as connected in how they change over time.

Sediment Supply to San Francisco Bay, Water Years 1995 through 2016: Data, trends, and monitoring recommendations to support decisions about water quality, tidal wetlands, and resilience to sea level rise

San Francisco Estuary Institute (SFEI) | June 11th, 2018

Knowledge of the status and trends of sediment supply to San Francisco Bay is critically important for management decisions about dredging, marsh restoration, flood contr

Knowledge of the status and trends of sediment supply to San Francisco Bay is critically important for management decisions about dredging, marsh restoration, flood control, contaminants, water clarity (in relation to primary production), and sea level rise. Several site-specific studies of sediment supply to San Francisco Bay have been conducted, but no synthesis of recent studies is available. The purpose of this report is to synthesize the best available data and knowledge to answer a few of the key study questions related to sediment supply to the Bay (listed below). This synthesis report was prepared jointly by the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) and the U. S. Geological Survey (USGS) with funding from both organizations. The project is meant to be a step in the development of a more comprehensive sediment management and monitoring strategy for the Bay.

Select Water Quality Parameters During Wet and Dry Conditions in the Colorado River Delta

American Water Resources Association (AWRA) | August 27th, 2022

Selenium Hazards in the Salton Sea Environment— Summary of Current Knowledge to Inform Future Wetland Management

U.S. Geological Survey (USGS) | July 20th, 2023

Quaternary marine and continental shales in the western United States are sources of selenium that can be loaded into the aquatic environment through mining, agricultural

Quaternary marine and continental shales in the western United States are sources of selenium that can be loaded into the aquatic environment through mining, agricultural, and energy production processes. The mobilization of selenium from shales through agricultural irrigation has been recognized since the 1930s; however, discovery of deformities in birds and other wildlife using agricultural habitats during the 1980s spurred studies to determine the extent and effects of the contamination. Through these early studies, researchers determined that biota in the Salton Sea drainage basin was at risk from legacy selenium contamination in the Colorado River watershed.

Shifting shores: Marsh expansion and retreat in San Pablo Bay

San Francisco Estuary Institute (SFEI) | June 30th, 2015

As sea level rise accelerates, our shores will be increasingly vulnerable to erosion. Particular concern centers around the potential loss of San Francisco Bay’s much-v

As sea level rise accelerates, our shores will be increasingly vulnerable to erosion. Particular concern centers around the potential loss of San Francisco Bay’s much-valued tidal marshes, which provide natural flood protection to our shorelines, habitat for native wildlife, and many other ecosystem services. Addressing this concern, this study is the first systematic analysis of the rates of marsh retreat and expansion over time for San Pablo Bay, located in the northern part of San Francisco Bay. Key findings: • Over the past two decades, more of the marshes in San Pablo Bay have expanded (35% by length) than retreated (6%). • Some areas have been expanding for over 150 years. • Some marsh edges that appear to be retreating are in fact expanding rapidly at rates of up to 8 m/yr. • Marsh edge change may be a useful indicator of resilience, identifying favorable sites for marsh persistence. • These data can provide a foundation for understanding drivers of marsh edge expansion and retreat such as wind direction, wave energy, watershed sediment supply, and mudflat shape. • This understanding of system dynamics will help inform management decisions about marsh restoration and protection. • This study provides a baseline and method for tracking marsh edge response to current and future conditions, particularly anticipated changes in sea level, wave energy, and sediment supply. Recommended next steps: • This pilot study for San Pablo Bay marshes should be extended to other marshes in San Francisco Bay. • These initial marsh expansion and retreat findings should be further analyzed and interpreted to improve our understanding of system drivers and identify management responses. • A program for repeated assessment should be developed to identify and track changes in shoreline position, a leading indicator of the likelihood marsh survival.

Simulated Effects of Future Water Availability and Protected Species Habitat in a Perennial Wetland, Santa Barbara County, California

Water (MDPI) | April 21st, 2025

This study evaluates the potential water availability in Barka Slough and the effects of changing hydrological conditions on the aquatic habitat of five protected species

This study evaluates the potential water availability in Barka Slough and the effects of changing hydrological conditions on the aquatic habitat of five protected species.

Sniffing the Delta for Greenhouse Gases

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

Global food production contributes an estimated 21% to 37% of the greenhouse gases that are warming the planet, including huge releases of carbon when vast aquatic ecosys

Global food production contributes an estimated 21% to 37% of the greenhouse gases that are warming the planet, including huge releases of carbon when vast aquatic ecosystems like the Delta are transformed for agriculture. [Dennis] Baldocchi and colleagues are now trying to figure out if bringing back tidal wetlands like the one at Dutch Slough can help reverse these processes.