Review our work products
We provide easy access to thousands of SFEI’s reports, journal articles, books, conference papers/proceedings, factsheets, hearing summaries, maps, and more.
These printable and downloadable materials connect our science to action, cover a broad range of topics, and have many applications. This library is searchable and filterable. If you have difficulty finding the information you are looking for, please contact us at [email protected].
Programs & Topics
Select the program or topic of your interest among the nested filters below.
Author(s): Martin Trinh | Amy Kleckner | Jay Davis | Alicia Gilbreath | Donald Yee | Miguel Méndez | Ezra Miller | Rebecca Sutton | Jennifer Dougherty
2026
The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) has conducted long-term contaminant monitoring in San Francisco Bay waters since 1993 through its Status and Trends (S&T) program. Following a 2020 program review and growing concern that urban…
Author(s): Martin Volaric | Ariella Chelsky | David Senn
2026
In August 2022, San Francisco Bay (SFB) experienced an overgrowth of the raphidophyte Heterosigma akashiwo, resulting in the most extensive harmful algal bloom (HAB) on record. The progression of the bloom, and associated parameters including concentrations of dissolved…
Bay Regional Monitoring Program Sediment Workgroup Management Questions 1 & 2 Update and Workplan
Author(s): Melissa Foley | Scott Dusterhoff | Lester McKee
2026
The goal of this update and workplan is to document the process used to update Management Questions s 1 and 2 and develop science questions, as well as articulate a 5-year workplan the Sediment Workgroup of the Regional Monitoring Program for Water Quality in San Francisco…
Author(s): Amy Kleckner | Jennifer Dougherty | Sasha Mariniuk
2026
In 2016, the State Water Resources Control Board approved a selenium TMDL for North San Francisco Bay. The TMDL established a target concentration of 11.3 μg/g dw in white sturgeon muscle tissue as the basis for evaluating impairment (SFBRWQCB 2015). Following discussions…
Author(s): Dan Killam | David Senn | Lindsey Sim | Raphael Kudela | Richard Stumpf | Shelly Tomlinson | Andrew Meredith | Brian Bergamaschi | Tamara Krauss | Katy O'Donnell
2026
This project represents the first effort to use satellite data to create a long-term, multi-satellite San Francisco Bay-specific turbidity dataset. Having accurate turbidity data will ultimately improve estimates of long-term gross primary productivity, and allow…
Author(s): Anna Mahony | Miguel Méndez | Rebecca Sutton | Patrick McNamara | William Arnold
2026
Quaternary ammonium compounds (QACs) are widely used and have numerous routes to the environment. This work assessed the levels of QACs in surface waters that receive treated wastewater effluent. Samples were collected over a 27 months period from eight different surface…
Author(s):
2026
This Program Plan summarizes the planned work for the San Francisco Bay Nutrient Management Strategy (NMS) Program during Fiscal Year 2027 (July 1, 2026 through June 30, 2027). The planned work includes a suite of projects and priorities targeting 2025-2030 NMS Management…
Moored Sensor Program Semi-annual Report November 2025 - March 2026
Author(s): Charlotte Diamant | Dan Killam | Ariella Chelsky | Katie Noland | Lucy Montgomery | Martin Volaric | Camille Michalak | Ben Hodder
2026
This report provides an overview of the Nutrient Management Strategy Moored Sensor Program's major accomplishments and findings between November 2025 and March 2026. Highlights include installing a new station in San Pablo Bay, installing a new station at the northern end of…
Author(s): Matthew Heberger | Lester McKee
2026
This document outlines a strategy of the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) for developing an integrated system of watershed and in-Bay models to help answer key management questions and support water quality protection and restoration…
Author(s): Ezra Miller | Sierra Garcia | Ruth Askevold | Jennifer Symonds | Rebecca Sutton
2026
In 2018, the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) launched an innovative investigation to detect contaminants that were either new to Bay sediment or had previously gone undetected. This study used nontarget analysis, a powerful tool that…
Regional Monitoring Program for Water Quality in San Francisco Bay Communication Strategy
Author(s): Sierra Garcia | Jay Davis
2026
Communicating information in support of management decisions is a key element of the Regional Monitoring Program for Water Quality in San Francisco Bay. Although the Program has always prioritized high-caliber communication outputs, 2025 is the first time staff capacity has…
Author(s): Amy Kleckner | Jay Davis
2026
The purpose of this document is to guide efforts and summarize plans developed within the RMP. The intended audience includes representatives of the many organizations who directly participate in the Program. This document will also be useful for individuals who are not…
Author(s): Amy Kleckner | Jay Davis
2026
In 2026, the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is entering its 34th year of collecting data and communicating information to support water quality management decisions. This Detailed Workplan and Budget describes the activities that will…
Updates to Moored Sensor Program Calibration and Data QAQC Procedures (2025)
Author(s): Martin Volaric | Katie Noland | Lilia Mourier | David Senn | Ariella Chelsky
2025
The San Francisco Bay (SFB) Nutrient Management Strategy maintains an extensive array of in situ data sondes for water quality monitoring as a part of its Moored Sensor Program (MSP). This report describes new calibrations for three of these sonde types. It also documents a…
Evaluation of the Chronic Toxicity of San Francisco Estuary Ambient Waters
Author(s): Stephen Clark
2025
As part of the San Francisco Estuary RMP 2025 Summer Cruise monitoring, Pacific EcoRisk (PER) was contracted to perform evaluations of the chronic toxicity of ambient waters collected from the San Francisco Estuary system in August and September of 2025. These evaluations…
Author(s): Anna Mahony | Tyler Clair | Miguel Méndez | Patrick McNamara | William Arnold
2025
Quaternary ammonium compounds (QACs) are high production volume chemicals used in consumer and industrial products, including disinfectants. Influent, effluent, and biosolid samples were collected from 12 wastewater treatment plants (WWTPs) from 2020 to 2023 and analyzed for…
The Carquinez Strait Fish and Preservation Project: Contaminant Concentrations in Fish
Author(s): Martin Trinh | Jay Davis | Miguel Méndez | Donald Yee | Adam Wong | LaDonna Williams | Joe Clark | Rick Wilder | Andrew Kalmbach | Autumn Bonnema | Wes Heim | Richard Grace
2025
This report presents the results of a community-led effort to assess contaminant concentrations in fish collected from the Carquinez Strait in 2023–2024. The project was conducted to fill critical data gaps for contaminants of concern, including mercury, polychlorinated…
Author(s): San Francisco Estuary Institute (SFEI)
2025
The overarching goal of the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is to answer the highest priority scientific questions faced by managers of Bay water quality. The RMP is an innovative collaboration between the San Francisco Bay Regional…
Comparison of creek and bay influences on salt marsh sediment budget and deposition patterns
Author(s): Lukas WinklerPrins | Jessica Lacy | Mark Stacey | Karen Thorne | McKenna Bristow | Scott Jones
2025
The resilience of salt marshes with low organic production depends on their effective capture and retention of mineral sediment from adjacent waters. Little prior work has directly compared mechanisms of sediment import from wave-influenced marsh boundaries against those of…
Author(s): Miguel Méndez | Jay Davis | Ezra Miller | Richard Grace | Rebecca Sutton
2025
Consumption of contaminated food, especially seafood, is a key source of human perfluoroalkyl and polyfluoroalkyl
substances (PFAS) exposure. Here, we examine the occurrence of PFAS in shiner surfperch (Cymatogaster aggregata), striped bass (Morone saxatilis…
Integrated Watershed Modeling and Monitoring Framework to Support the Regional Monitoring Program
Author(s): Lester McKee | Kelly Moran | Jay Davis
2025
The Regional Monitoring Program (RMP) is transitioning from a watershed program predominantly using monitoring data and data-driven load estimation methods to support management decisions on polychlorinated biphenyls (PCBs) and mercury (Hg) to an integrated modeling and…
Author(s): Amy Kleckner | Jay Davis
2025
In 2025, the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is
entering its 33rd year of collecting data and communicating information to support water
quality management decisions. This Detailed Workplan and Budget describes the activities…
Author(s): Amy Kleckner | Jay Davis
2025
The purpose of this document is to guide efforts and summarize plans developed within the RMP. The intended audience includes representatives of the many organizations who directly participate in the Program. This document will also be useful for individuals who are not…
Author(s): Pedro Avellaneda | Lorenzo Flores | Lester McKee
2025
The San Francisco Bay Regional Watershed Spreadsheet Model (RWSM) was developed within the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) to estimate average annual regional and sub-regional scale pollutant loads to the Bay from stormwater. The RWSM…
Continuous Suspended Sediment Monitoring in South and Lower South San Francisco Bay Final Report
Author(s): Martin Volaric | Lilia Mourier | Lucy Montgomery | Katie Noland | David Senn | Ariella Chelsky
2025
This report presents results from a three-year effort (2022-2024) to estimate continuous suspended sediment concentration (SSC) in the South Bay (SB) and Lower South Bay (LSB) regions of San Francisco Bay (SFB). We used discrete SSC samples to calibrate high-frequency (15-min…
Charter: Regional Monitoring Program for Water Quality in San Francisco Bay
Author(s): Jay Davis | Amy Kleckner
2025
This Charter describes the purpose and function of the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). Established in 1993, the RMP is a collaborative effort between the San Francisco Estuary Institute, the California Regional Water Quality Control…
Author(s): Sam McWilliams | Kara Scheu | Craig Jones | Donald Yee | Allie King | Jay Davis
2024
Modeling of fate and transport in San Francisco Bay is needed to address many priority management questions that have been articulated by RMP workgroups for PCBs, sediment, and contaminants of emerging concern (CECs). This report is part of a first phase of implementation of…
Author(s): Melissa Foley | Jay Davis | Rebecca Sutton | Donald Yee
2024
In 2020, the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) undertook a review of the Status and Trends (S&T) Program, a vital component of the RMP. The goals of the S&T Program are to measure contaminant concentrations in San Francisco Bay…
Author(s):
2024
This report provides information about sportfish monitoring collection conducted by ICF during 2024 for the San Francisco Estuary Institute (SFEI) as part of the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). The RMP monitors spatial patterns and…
San Francisco Bay Triennial Bird Egg Monitoring Program for Contaminants - 2024 Data Summary
Author(s): Joshua Ackerman | Alex Hartman | Mark Herzog | Brady Fettig
2024
The USGS's long-term Wildlife Contaminants Program in collaboration with the San Francisco Bay Regional Monitoring Program (RMP) collects bird eggs throughout the San Francisco Bay Estuary to assess temporal trends in contaminant concentrations. This document…
Author(s): Amy Kleckner | Donald Yee | Rebecca Sutton | Jay Davis
2024
This document details sampling and analysis plans associated with triennial monitoring of contaminants in bird egg tissue for the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). In 2024 staff at the USGS Western Ecological Research Center (USGS-WERC)…
Author(s): Martin Trinh | Donald Yee | Amy Kleckner | Jay Davis | Autumn Bonnema | Rick Wilder
2024
This document details sampling and analysis plans associated with the Status and Trends (S&T) sport fish contaminant monitoring for the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). Fish will be collected from various locations in the Bay.…
Screening Bay Area Stormwater for Emerging Contaminants: Summary for Managers
Author(s): Rebecca Sutton | Pedro Avellaneda | Miguel Méndez | Jennifer Dougherty | Alicia Gilbreath
2024
As part of a maturing science strategy, the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) focuses on monitoring and modeling of emerging contaminants in major pathways in an effort to track Bay contaminants back to their sources and better inform…
Author(s): Jennifer Dougherty | Diana Lin | Ezra Miller | Rebecca Sutton | Samantha DiLoreto | Kirsten Overdahl | Bernadette Vogler | Lee Ferguson
2024
Ethoxylated surfactant compounds are a broad class of non-ionic surfactants that include alkylphenol ethoxylates (APEOs) and alcohol ethoxylates (AEs). Together, APEOs and AEs are used in a wide range of consumer and industrial applications as emulsifiers, wetting agents,…
Author(s): Alicia Gilbreath | Lester McKee | Matthew Heberger | Kelly Moran
2024
The Sources, Pathways, and Loadings (SPL) Workgroup (WG) is one of the five active workgroups within the Regional Monitoring Program for Water Quality in San Francisco Bay (Bay; RMP). The Workgroup produces recommendations for collection, interpretation, and synthesis of data…
Author(s): Kyle Stark | David Peterson | Alicia Gilbreath | Emma Sevier | Scott Dusterhoff
2024
SFEI worked in partnership with Balance Hydrologics, Inc. to collect flow and sediment data on Pescadero Creek during Water Years 2023 and 2024, focused on high-flow periods. SFEI then developed a discharge-SSC rating curve for Pescadero Creek. Sediment loads on Pescadero…
Author(s): David Peterson | Kyle Stark | Alicia Gilbreath | Scott Dusterhoff
2024
This low-flow conditions report of Pescadero Creek was created to improve our understanding of flow and sediment dynamics during low-discharge periods near the mouth of Pescadero Creek to support management related to the 2018 Pescadero-Butano Sediment TMDL Habitat…
Author(s): Yeo Cho | Diana Lin | Donald Yee | Jay Davis | Richard Luthy
2024
To assess historical PCB loading and spatial distribution in the Steinberger Slough and Redwood Creek (SS/RC) complex, a passive sampling campaign was conducted in the summer of 2020 at eight selected sites. Passive sampler uptakes (CPE) successfully captured PCB distribution…
Author(s): Diana Lin | Miguel Méndez | Kayli Paterson | Adam Wong | Donald Yee | Rebecca Sutton | Erika Houtz | Mary Cousins | Lorien Fono
2024
Identification of major sources of per- and polyfluoroalkyl substances (PFAS) in wastewater requires comprehensive evaluation, as wastewater is a pathway for a wide range of PFAS products in use, and the PFAS class includes thousands of compounds. We applied both EPA Method…
Author(s): San Francisco Estuary Institute (SFEI)
2024
The theme of the 2024 Pulse is "Contaminants of Emerging Concern." The 2013 edition of the Pulse was the first to focus on contaminants of emerging concern (CECs), with the goal of providing an overview of past RMP work, future plans, and a…
Author(s): Rebecca Sutton | Ezra Miller | Miguel Méndez | Adam Wong | Kayli Paterson | Jennifer Dougherty | Diana Lin
2024
Over 350,000 chemicals and mixtures of chemicals have been registered for production and use worldwide. A portion of these may meet the definition of contaminants of emerging concern (CECs), chemicals that are unregulated or under-regulated, not commonly monitored in…
Author(s): Jennifer Dougherty | Miguel Méndez | Ezra Miller | Rebecca Sutton
2024
Chlorinated paraffins are a class of mixtures of chlorinated hydrocarbons that are produced and used globally at high volumes for various consumer and industrial applications. Chlorinated paraffins are composed of short-chain (SCCPs), medium-chain (MCCPs), and long-chain…
Implementing Nature-based Solutions for Wastewater Management: San Francisco Bay Area Examples
Author(s): G. Miller | Annie Sneed | Ellen Plane | Ian Wren
2024
Prepared by the San Francisco Estuary Institute for the Bay Area Clean Water Agencies.
Prepared in partnership with City of Hayward, City of Petaluma, East Bay Dischargers Authority, East Bay Regional Park District, Las Gallinas Valley Sanitary District, Mountain…
Author(s): Katherine Peter | Alicia Gilbreath | Melissa Gonzalez | Zhenyu Tian | Adam Wong | Donald Yee | Ezra Miller | Pedro Avellaneda | Da Chen | Andrew Patterson | Nicole Fitzgerald | Christopher Higgins | Edward Kolodziej | Rebecca Sutton
2024
In urban to peri-urban watersheds such as those surrounding San Francisco Bay, stormwater runoff is a major pathway by which contaminants enter aquatic ecosystems. We evaluated the occurrence of 154 organic contaminants via liquid chromatography coupled to tandem mass…
Study of Per- and Polyfluoroalkyl Substances in Bay Area POTWs: Final Report
Author(s): Diana Lin | Miguel Méndez | Kayli Paterson
2024
Per- and polyfluoroalkyl substances (PFAS) are a broad class of fluorine-rich specialty chemicals with many uses across consumer, commercial, and industrial applications and products. The carbon-fluorine bonds that define this class afford PFAS stability during use and…
Author(s): Donald Yee | Adam Wong
2024
San Francisco Bay margins (i.e., mudflats and adjacent shallow areas of the Bay that are shallower than 1 foot below mean lower low water [MLLW]) are important habitats with high potential for aquatic life to be exposed to contaminants. These areas were not routinely sampled…
Author(s): Anna Mahony | William Arnold | Miguel Méndez | Ezra Miller | Rebecca Sutton
2024
Quaternary ammonium compounds (QACs) are surfactants widely used in a variety of consumer products, particularly as antimicrobials. The COVID-19 pandemic has increased use of products containing QACs. This is of concern because QACs can be toxic to aquatic life at low…
Author(s): Lilia Mourier | Lucy Montgomery | Martin Volaric | Ariella Chelsky | David Senn
2024
This report provides a project update for year two of a three-year collaboration between the San Francisco Bay Nutrient Management Strategy (NMS), San Francisco Bay Regional Monitoring Program, and South Bay Salt Pond Restoration Project, to estimate high frequency suspended…
Author(s): Amy Kleckner | Jay Davis
2024
The purpose of this document is to guide efforts and summarize plans developed within the RMP. The intended audience includes representatives of the many organizations who directly participate in the Program. This document will also be useful for individuals who are not…
Selenium Concentrations in Water and Clams in North San Francisco Bay, 2019-2020
Author(s): Melissa Foley | Jay Davis | Nina Buzby
2024
The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) started implementing a new design for North Bay selenium (Se) sampling in 2019 after a long-term USGS program was terminated in 2017. To determine if the RMP sampling and analysis methods are…
Water Year 2024 RMP Near-Field Water Sampling and Analysis Plan
Author(s): Jennifer Dougherty | Amy Kleckner | Rebecca Sutton | Donald Yee | Alicia Gilbreath | Martin Trinh
2024
This report details sampling and analysis plans associated with the pilot near-field water sampling for the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). The RMP added a pilot effort to the Status & Trends (S&T) Program to…
Author(s): Paul Mayer | Kelly Moran | Ezra Miller | Susanne Brander | Stacey Harper | Manuel Garcia-Jaramillo | Victor Carrasco-Navarro | Kay Ho | Robert Burgess | Leah Hampton | Elise Granek | Margaret McCauley | Jenifer McIntyre | Edward Kolodziej | Ximin Hu | Antony Williams | Barbara Beckingham | Miranda Jackson | Rhea Sanders-Smith | Chloe Fender | George King | Michael Bollman | Sujay Kaushal | Brittany Cunningham | Sara Hutton | Jackelyn Lang | Heather Goss | Samreen Siddiqui | Rebecca Sutton | Diana Lin | Miguel Mendez
2024
About 3 billion new tires are produced each year and about 800 million tires become waste annually. Global dependence upon tires produced from natural rubber and petroleum-based compounds represents a persistent and complex environmental problem with only partial and often…
Author(s): Allie King | Farid Karimpour | P Mugunthan | David Senn
2023
- 2023_SFEI_BGC_Modeling_Update_Report_20230127_0.pdf
- Appendix_A1.pdf
- Appendix_A2.pdf
- Appendix_A3.pdf
- Appendix_B_Stratification.pdf
- Appendix_C_POTW BC Time Series from WY2013-WY2018.pdf
- Appendix_D_WY2017_BGC Validation.pdf
- Appendix_E_WY2013_BGC Validation.pdf
- Appendix_F_BGC_Validation_Scatter.pdf
- Appendix_G.pdf
Carquinez Strait Fish and Preservation Project Fish Collection Summary Report
Author(s): ICF
2023
In 2023, San Francisco Estuary Institute (SFEI) received funding from a grant won by All Positives Possible, a nonprofit organization with 501c3 status, to provide shoreline education, fish testing, garbage abatement, and preservation process that is engaging members and…
Author(s): David Peterson | Kyle Stark | Jim Robins | Scott Dusterhoff | Kendall Harris
2023
SFEI developed a protocol for field-based techniques to quantify in-stream large wood for Pescadero and Butano creeks and their tributaries in San Mateo County, California. The protocol was designed to capture multifaceted data and can be used to assess large wood loading…
2023 Bay Prey Fish and Near-field / Margins Sediment Sampling and Analysis Plan
Author(s): Miguel Mendez | Amy Kleckner | Rebecca Sutton | Donald Yee | Adam Wong | Jay Davis | Marco Sigala
2023
This is a sampling and analysis plan for the Bay Status and Trends (S&T) Prey Fish and Near-field / Margins Sediment monitoring for the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). Bay margins are defined by the RMP as extending from Mean…
Author(s): Amy Kleckner | Rebecca Sutton | Donald Yee | Adam Wong | Jay Davis | Paul Salop
2023
This report details plans associated with the 2023 Regional Monitoring Program for Water Quality in the San Francisco Estuary (RMP) water cruise. The RMP water sampling program was redesigned in 2002 to adopt a randomized sampling design at thirty-one stations in place of the…
2023 RMP Margins & Nearfield Sediment and Prey Fish Cruise Report
Author(s):
2023
This report contains information on the summer 2023 field sampling efforts conducted by the San Jose State University Research Foundation’s (SJSURF) Marine Pollution Studies Lab at Moss Landing Marine Labs (MPSL-MLML) in support of the Regional Monitoring Program’s (RMP)…
Author(s):
2023
This report outlines details from the annual Regional Monitoring Program for Water Quality in the San Francisco Estuary (RMP) sediment cruise, conducted July 24 – 27, 2023. The Regional Monitoring Program conducts routine monitoring of water, sediment and biological tissue.…
Author(s): Amy Kleckner | Rebecca Sutton | Donald Yee | Adam Wong | Jay Davis | Paul Salop
2023
This report details plans associated with the Regional Monitoring Program for Water Quality in the San Francisco Estuary (RMP) deep bay sediment cruise. The RMP, through the Status and Trends monitoring program, conducts routine monitoring of water, sediment and biological…
Author(s): San Francisco Estuary Institute (SFEI)
2023
The overarching goal of the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is to answer the highest priority scientific questions faced by managers of Bay water quality. The RMP is an innovative collaboration between the San Francisco Bay Regional…