San Francisco Bay

Emerging PFAS Trends in Water and Sediment from San Francisco Bay

San Francisco Estuary Institute (SFEI) | August 14th, 2025

Per- and polyfluoroalkyl substances (PFAS) are a diverse class of persistent compounds, including several that are bioaccumulative and known or suspected to be toxic. The

Per- and polyfluoroalkyl substances (PFAS) are a diverse class of persistent compounds, including several that are bioaccumulative and known or suspected to be toxic. These unique compounds have widespread uses across consumer, commercial, and industrial products, resulting in widespread occurrence in humans, the environment, and wildlife across the globe. Within San Francisco Bay, the RMP has monitored PFAS across the Bay ecosystem, beginning in 2004 with various biota and since expanding to sediment, surface water, stormwater, and wastewater. These studies found PFAS throughout the Bay, especially in sport fish, where concentrations are of potential concern for human health and led to a classification of PFAS as High Concern for the Bay under the RMP tiered risk-based framework for emerging contaminants.  This study examined Bay sediment and surface water to continue to build our understanding of the occurrence, fate, and risks of PFAS to ecological and human health. Using a targeted method, 40 PFAS were analyzed in Bay sediment collected in three monitoring cruises from 2017 to 2023, and Bay water collected from 2021 to 2023 during both the dry and wet seasons. The Total Oxidizable Precursor (TOP) assay was also used to supplement these findings by indirectly measuring unknown perfluoroalkyl acid (PFAA) precursors of detectable PFAS. This additional information aids in elucidating the broader levels of PFAS present in samples to better evaluate the exposure and risk to the Bay. 

Emerging understanding of the potential role of seagrass and kelp as an ocean acidification management tool in California

California Ocean Science Trust (OST) | January 2nd, 2018

This report was produced by the OPC-SAT working group and Ocean Science Trust on behalf of the Ocean Protection Council (OPC) and the broader community of California man

This report was produced by the OPC-SAT working group and Ocean Science Trust on behalf of the Ocean Protection Council (OPC) and the broader community of California managers with the aim of: • communicating emerging scientific understanding of the ability of seagrass and macroalgae (kelps) to ameliorate ocean acidification (OA) in a California-specific context, • summarizing knowledge gaps and opportunities for filling them through research and monitoring, and • providing guidance on next steps for the State as it considers future nature-based actions to reduce the negative impacts of OA in California and beyond.

Empirical and Experimental Analyses of Secondary Louver Efficiency at the Tracy Fish Collection Facility: March 1996 to November 1997

U.S. Bureau of Reclamation (USBR) | January 30th, 2004

Empirical Models of Shallow Groundwater and Multi-Hazard Flood Forecasts as Sea-Levels Rise

American Geophysical Union (AGU) | February 8th, 2025

Knowledge of coastal hydrogeology and hazards as groundwater responds to sea-level rise (SLR) can be improved through installation of shallow groundwater monitoring piezo

Knowledge of coastal hydrogeology and hazards as groundwater responds to sea-level rise (SLR) can be improved through installation of shallow groundwater monitoring piezometers and continuous observations. Interpolation of site data enables mapping of the present-day state of groundwater elevation, depth to groundwater (DTW), their temporal statistical variation, and differing spatial responses to tides and rainfall. Future DTW and its variability can be projected under increments of SLR, with assumptions and caveats, to show where and when episodic and/or permanent inundation can be expected. This methodology is outlined in a case study of Dunedin, New Zealand, which enabled comparison of rising groundwater's contribution to pluvial flooding and groundwater emergence with coastal inundation. Changes in relative land exposure with SLR shows evolution in flood hazard from current pluvial-dominated events, into “flooding from below” and groundwater emergence, in advance of any overland coastal inundation. Dunedin exemplifies how groundwater transfers effects of SLR surprisingly far inland, but the lowest-lying or shoreline-proximal suburbs are not necessarily the most vulnerable. Unlike coastal inundation, rising groundwater is unconstrained by protective topography and presents as a creeping hazard, or contributor to hazards such as pluvial flooding, which can be widespread, occurring already and difficult to defend against. The empirical models contain assumptions and uncertainties important to the veracity of results and application. While conservative (“risk averse”) and a compromise from computationally expensive numerical solutions, their value is in providing the spatial and temporal precision needed for multi-source hazard assessment and holistic adaptive planning.

Endangered and Threatened Species: Status for the San Francisco Bay-Delta Distinct Population Segment of the Longfin Smelt

U.S. Fish and Wildlife Service (FWS) | February 27th, 2023

Endangered Species Status for the San Francisco Bay-Delta Distinct Population Segment of the Longfin Smelt

U.S. Fish and Wildlife Service (FWS) | July 30th, 2024

We, the U.S. Fish and Wildlife Service (Service), determine endangered species status under the Endangered Species Act of 1973, as amended (Act), for the San Francisco Ba

We, the U.S. Fish and Wildlife Service (Service), determine endangered species status under the Endangered Species Act of 1973, as amended (Act), for the San Francisco Bay-Delta distinct population segment (DPS) of longfin smelt (Spirinchus thaleichthys), a fish species of the Pacific Coast. This rule extends the protections of the Act to this DPS and adds it to the List of Endangered and Threatened Wildlife.... This final rule is available on the internet at https://www.regulations.gov. Comments and materials we received on the proposed rule are available for public inspection at https://www.regulations.gov at Docket No. FWS-R8-ES-2022-0082. Availability of supporting materials: Supporting materials we used in preparing this rule, such as the species status assessment report, are available at https://www.regulations.gov at Docket No. FWS-R8-ES-2022-0082.

Energy Down the Drain. The Hidden Costs of California's Water Supply

Natural Resources Defense Council (NRDC) | August 2nd, 2004

California has been through its share of scorching droughts and energy shortages, but many residents of the western United States may not realize the close con- n

California has been through its share of scorching droughts and energy shortages, but many residents of the western United States may not realize the close con- nections between water and power resources. Water utilities use large amounts of energy to treat and deliver water. Even after utilities deliver water, consumers burn more energy to heat, cool, and use the water. The California State Water Project is the largest single user of energy in California. In the process of delivering water from the San Francisco Bay-Delta to Southern California, the project uses 2 to 3 percent of all electricity consumed in the state. The State Water Project burns energy pumping water 2,000 feet over the Tehachapi Mountains—the highest lift of any water system in the world. The amount of energy used to deliver that water to residential customers in Southern California is equivalent to approximately one-third of the total average household electric use in the region. Ninety percent of all electricity used on farms is devoted to pumping groundwater for irrigation.

Enhancements to EcoAtlas’ CRAM analysis tools: Habitat Development Curves and Ecoregional Cumulative Distribution Function plots (CDFs)

San Francisco Estuary Institute (SFEI) | April 5th, 2016

Enhancing the Vision for Managing California’s Environmental Information

Delta Stewardship Council (Delta Council) | July 1st, 2015

The Environmental Data Summit, convened under the auspices of the Delta Stewardship Council’s Delta Science Program in June 2014, witnessed remarkable participation fro

The Environmental Data Summit, convened under the auspices of the Delta Stewardship Council’s Delta Science Program in June 2014, witnessed remarkable participation from experts across California, the nation, and even the world. Summit attendees from the public, private, federal, and non-profit sectors shared their views regarding the urgent needs and proposed solutions for California’s data-sharing and data-integration challenges, especially pertaining to the subject of environmental resource management in the era of “big data.” After all, this is a time when our data sources are growing in number, size, and complexity. Yet our ability to manage and analyze such data in service of effective decision-making lags far behind our demonstrated needs. In its review of the sustainability of water and environmental management in the California Bay-Delta, the National Research Council (NRC) found that “only a synthetic, integrated, analytical approach to understanding the effects of suites of environmental factors (stressors) on the ecosystem and its components is likely to provide important insights that can lead to enhancement of the Delta and its species” (National Research Council 2012). The present “silos of data” have resulted in separate and compartmentalized science, impeding our ability to make informed decisions. While resolving data integration challenges will not, by itself, produce better science or better natural resource outcomes, progress in this area will provide a strong foundation for decision-making. Various mandates ranging from the California Water Action Plan to the President’s executive order demanding federal open data policies demonstrate the consensus on the merits of modern data sharing at the scale and function needed to meet today’s challenges. This white paper emerges from the Summit as an instrument to help identify such opportunities to enhance California’s cross-jurisdictional data management. As a resource to policymakers, agency leadership, data managers, and others, this paper articulates some key challenges as well as proven solutions that, with careful and thoughtful coordination, can be implemented to overcome those obstacles. Primarily featured are tools that complement the State’s current investments in technology, recognizing that success depends upon broad and motivated participation from all levels of the public agency domain. This document describes examples, practices, and recommendations that focus on California’s Delta as an opportune example likely to yield meaningful initial results in the face of pressing challenges.  Once proven in the Delta, however, this paper’s recommended innovations would conceivably be applied statewide in subsequent phases.

Environmental Characteristics of Select Managed Ponds in the Sacramento–San Joaquin Delta: Implications for Native Fish Conservation and Research

U.S. Geological Survey (USGS) | July 23rd, 2025

The use of wetlands to support native fish research and conservation efforts in the Sacramento–San Joaquin Delta (Delta) of California is a growing priority. The purpos

The use of wetlands to support native fish research and conservation efforts in the Sacramento–San Joaquin Delta (Delta) of California is a growing priority. The purpose of our study was to examine the physiochemical and biological characteristics of select managed ponds in the Delta to determine if they would be suitable habitats for research involving the conservation of delta smelt (Hypomesus transpacificus). We studied 10 managed ponds distributed across the central part of the Delta situated on Bacon Island and Bouldin Island in San Joaquin County, and Holland Tract and Webb Tract islands in Contra Costa County. The managed ponds had a diversity of physical habitat configurations and were not directly connected to waterways surrounding the islands and, therefore, not affected by tides. We studied the managed ponds from approximately November 2021 to December 2023 to assess water quality, zooplankton, fish, and pesticide metrics. Water levels in the managed ponds were managed to varying degrees and were mostly independent of climate-driven wet-dry seasonality. Water quality conditions varied among ponds and were independent of geographic location. Overall, mean monthly chlorophyll a concentration ranged from 15 to 57 (mean=30) micrograms per liter (μg/L), dissolved oxygen concentration ranged from 4 to 9 (mean=7) milligrams per liter (mg/L), pH was 8, salinity was 1 practical salinity units (PSU), specific conductance ranged from 1,202 to 1,839 (mean=1,471) microsiemens per centimeter (μS/cm), and turbidity ranged from 13 to 24 (mean=19) Formazin Nephelometric Units (FNU). Water temperature thresholds that contribute to stress (21 degrees Celsius [°C]) and mortality (28 °C) of delta smelt were often exceeded during summer and fall, though vertical stratification contributed to lower bottom temperatures in the deepest managed ponds, which could potentially provide thermal refugia for delta smelt so long as dissolved oxygen concentrations are suitable. Zooplankton populations were broadly similar among managed ponds and included calanoid and cyclopoid copepods that would be suitable prey for delta smelt. Overall average total zooplankton biomass, as measured with a Schindler-Patalas trap, was 0.6 μg/L (min=0, max=63.6) and peaked during spring at more than 4 μg/L. Fish populations highly varied among the managed ponds with potential predators of delta smelt such as largemouth bass (Micropterus salmoides) and black crappie (Pomoxis nigromaculatus) present in several of the managed ponds; predator distribution among ponds seemed to have been driven primarily by deliberate stocking to facilitate local fisheries. Measured pesticide concentrations were below U.S. Environmental Protection Agency Aquatic Life Benchmarks except for exceedances of three compounds (diuron [herbicide], clothianidin [insecticide], and deltamethrin [pyrethroid insecticide]) in samples collected from ponds on Bouldin Island and Webb Tract. Overall, most managed ponds seemed suitable to support delta smelt, though physical control of potential predators and summer temperature might be needed. The results provide guidance on how to engineer and manage new managed ponds to support research and conservation efforts for delta smelt and other native fishes.