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. 

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

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.

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 Baseline Biological Resources - Fauna, Total Water Management Study for the Central Valley, California

U.S. Bureau of Reclamation (USBR) | January 1st, 1975

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.

Environmental Water Account: Need for Legislative Definition and Oversight

Legislative Analyst's Office (LAO) | January 29th, 2001

We recommend that the Legislature hold oversight hearings to evaluate CALFED's proposal for the Environmental Water Account, implemented to acquire water for endangered s

We recommend that the Legislature hold oversight hearings to evaluate CALFED's proposal for the Environmental Water Account, implemented to acquire water for endangered species protection and recovery in the Bay-Delta region. There are many policy and implementation issues that the Legislature should consider before CALFED proceeds with the new program, including the program's costs, benefits, impacts, governance, and funding. Funding should be governed by the "beneficiary pays" principle.

Envisioning Futures for the Sacramento-San Joaquin Delta

Public Policy Institute of California (PPIC) | January 25th, 2007

California’s Sacramento-San Joaquin Delta is widely perceived to be in crisis today: its levee system is fragile, many of its native species are declining rapidly, and

California’s Sacramento-San Joaquin Delta is widely perceived to be in crisis today: its levee system is fragile, many of its native species are declining rapidly, and it lacks strong governing institutions to deal with its problems. In its current state, the Delta is unsustainable for almost all stakeholders. This report provides a comprehensive, scientifically up-to-date analysis and outlines several alternative management strategies for the Delta.

Estimates of Natural and Unimpaired Flows for the Central Valley of California: Water Years 1922-2014 (draft)

California Department of Water Resources (DWR) | March 1st, 2016

Estimating regional water supplies that would have occurred absent human activities is a common practice in water resources planning. In this report, such theor

Estimating regional water supplies that would have occurred absent human activities is a common practice in water resources planning. In this report, such theoretical water supply estimates are referred to as “unimpaired” flow. Since 1980, the Department of Water Resources (Department) has periodically published estimates of Central Valley unimpaired flows. In spite of the Department’s previous attempts to distinguish between natural conditions and its calcula tion of theoretical unimpaired flows, unimpaired flow estimates have frequently been used as a surrogate measure of natural conditions, presumably because natural flow estimates were unavailable. A major objective of this report is to clarify the conceptua l differences between natural and unimpaired flows. In this report, the term “unimpaired” flow is used to describe a theoretically available water supply assuming existing river channel conditions in the absence of (1) storage regulation for water supply a nd hydropower purposes and (2) stream diversions for agricultural and municipal uses. Unimpaired flow estimates are theoretical in that such conditions have not occurred historically. In pristine watersheds which have undergone little land use change, unim paired flow estimates provide a fixed frame of reference to develop relationships between precipitation, runoff, and water supply based on long - term hydrologic records. For many years these relationships were based on the assumption of stationarity, i.e. that the past is a good indicator of the future. However, global warming now requires hydrologists and water resources managers to analyze non-stationary processes, requiring more sophisticated tools and techniques to quantify future water supplies. This report updates and extends the Department’s previous published estimates of unimpaired flows for 24 Central Valley sub-basins and the Delta. Monthly unimpaired flows are presented for water years 1922 - 2014.