Our Program and Focus Areas

RMP LogoThe Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is SFEI’s largest program. It provides the information that regulators and decision-makers need to manage the Bay effectively. The RMP is an innovative collaborative effort between SFEI, the Regional Water Quality Control Board, and the regulated discharger community.

An innovative partnership

The RMP has combined shared financial support, direction, and participation by regulatory agencies and the regulated community in a model of collective responsibility. The RMP has established a climate of cooperation and a commitment to participation among a wide range of regulators, dischargers, industry representatives, non-governmental agencies, and scientists. The RMP provides an open forum for interested parties to discuss contaminant issues facing the Bay.

An adaptive, long term program of study in support of management

Stable funding has enabled the RMP to develop long-term plans. In addition, Special Studies provide an opportunity to adapt to changing management priorities and advances in scientific understanding. RMP committees and workgroups meet regularly to keep the Program efficient, focused on the highest priority issues, and to ensure that RMP science is sound. The RMP has continually improved since its inception in 1993.

A high quality body of knowledge

The RMP has produced a world-class dataset on estuarine contaminants. Monitoring performed in the RMP determines spatial patterns and long-term trends in contamination through sampling of water, sediment, bivalves, bird eggs, and fish, and evaluates toxic effects on sensitive organisms and chemical loading to the Bay. The Program combines RMP data with data from other sources to provide for comprehensive assessment of chemical contamination in the Bay.

A portal to information about contamination in San Francisco Bay

The RMP provides information targeted at the highest priority questions faced by managers of the Bay. The RMP produces summary reports (Pulse of The Bay and RMP Update), technical reports that document specific studies and synthesize information from diverse sources, as well as journal publications that disseminate RMP results to the world’s scientific community. The RMP website provides access to RMP data, information products, and links to other sources of information about water quality in San Francisco Bay.

Events and Meeting Materials

Focus areas covered by the RMP are primarily addressed by the six workgroups: Emerging Contaminants (ECWG); Exposure and Effects (EEWG); Sources, Pathways and Loadings (SPLWG); PCBs; Selenium; and Dioxin. Workgroups consist of scientists who are currently studying the Bay, invited scientists who are nationally recognized experts in their field, and federal and state regulators. Each workgroup meets one to three times a year to address issues concerning the planning and implementation of RMP Special Studies and relevant elements of Status and Trends monitoring.

RMP "strategy teams" provide a forum for focus on specific interests to the program. The strategy teams are composed of stakeholder groups, which meet as needed to develop long-term RMP study plans for addressing high priority topics. To date, the RMP has developed strategies pertaining to mercury, PCBs, dioxins, small tributary loads, forecasting, and sport fish. The RMP also participates in the San Francisco Bay Nutrient Science and Management Strategy, which is developing the science needed for informed decisions about managing nutrient loads and maintaining beneficial uses within the Bay.

Activities of the workgroups, and technical content of the program as a whole, are overseen by the Technical Review Committee. The Steering Committee determines the overall budget, allocates program funds, tracks progress, and provides direction to the Program from a manager's perspective.


Key Resources


Events and Meeting Materials

In 1997, the RMP underwent a 5-year program review which helped to develop a revised set of RMP objectives including a new objective: “Describe general sources and loading of contamination to the Estuary” (Bernstein and O’Connor, 1997). The goal was to create a functional connection between the RMP and efforts to identify, eliminate, and prevent sources of pollution that influence the Bay. Guided by the new objective, the Sources, Pathways, and Loading Workgroup (SPLWG) was formed in early 1999 to produce recommendations for collection, interpretation, and synthesis of data on general sources and loading of trace contaminants to the Estuary. The first SPLWG recommendations were described in the first “Technical Report of the Sources Pathways and Loadings Workgroup” (Davis et al., 1999). Since that time the SPLWG has continued to provide management context and technical review on a series of desktop and field studies that largely followed the recommendations of Davis et al. (1999). The SPLWG ensures that the projects and products are relevant and help to answer ever developing management questions in the context of TMDLs and attainment of water quality standards.

In addition to it's other work, the SPLWG also oversees the Small Tributaries Loading Strategy (STLS) project. The STLS focuses on loadings from small tributaries (the rivers, creeks, and storm drains that enter the Bay downstream of Chipps Island), in coordination with the Municipal Regional Permit for Stormwater (MRP).

The scientific advisory panel consists of internationally known experts in this field including:

  • Dr. Barbara Mahler, US Geological Survey
  • Dr. Dan Cain, US Geological Survey
  • Dr. Tom Jobes
  • Dr. Dan Wang, CA Department of Pesticide Regulation


Lead Scientist: Lester McKee

For further information, please contact Lester McKee at: ph 510-746-7363 or [email protected].

The Bay RMP fills critical science needs to assist managers in their goal of reducing harmful emerging contaminants in San Francisco Bay. Emerging contaminants are unregulated or under-regulated and not commonly monitored, yet may pose significant ecological and/or human health risks.

A global leader in this field, the Bay RMP has developed an emerging contaminants strategy that guides decisions on monitoring and management. Early identification of problem pollutants and quick action to prevent their spread is an optimal and cost-effective approach for protecting water quality. This is especially true in an ecosystem like the Bay, which can act as a long-term trap for persistent contaminants, with recovery taking decades or centuries when contamination is extensive.

Diligent surveillance using state-of-the-art analytical techniques has identified emerging contaminants of moderate concern for the Bay:

  • PFAS, stain and water repelling chemicals widely used in industrial and consumer products
  • Fipronil and imidacloprid, insecticides with significant urban uses
  • Alkylphenols and alkylphenol ethoxylates, ingredients in detergents and many other products
  • Bisphenols, plastic ingredients
  • Organophosphate esters, flame retardants and plasticizers

 A scientific advisory panel of internationally renowned experts advises the Bay RMP Emerging Contaminants Workgroup (ECWG):

  • Dr. Bill Arnold, University of Minnesota
  • Dr. Miriam Diamond, University of Toronto
  • Dr. Lee Ferguson, Duke University
  • Dr. Derek Muir, Environment and Climate Change Canada
  • Dr. Heather Stapleton, Duke University
  • Dr. Dan Villenueve, US EPA

Lead Scientist: Rebecca Sutton, Ph.D.

PCBs are a pollutant of high concern in San Francisco Bay. Additionally, the bay was placed on the State of California’s 303(d) list of impaired waterways in 1998 as a result of elevated concentrations of dioxins and furans (commonly referred to as only ‘dioxin’) in fish. The PCB & Dioxin strategy ensures that the RMP is providing the information needed to support the development of appropriate effluent limits for municipal and industrial discharges and find remedies to the Bay’s PCB problem. The upcoming management decisions include the next iteration (2020-2021) of the PCB TMDL and identifying the best options for management actions to reduce PCB impairment. Our understanding of dioxin in the Bay has improved due to special studies conducted over the past decade. Although the available information suggests progress will be slow toward Bay-wide reductions in concentrations in fish and resulting health risks to humans and wildlife, similar to PCBs, there may be localized opportunities to effect change at select, more highly impacted, sites.

The scientific advisory panel for the Bay RMP PCBs & Dioxin Workgroup consists of:

Dr. Frank Gobas, Simon Fraser University

Lead Scientist: Jay Davis

For more information, please contact Jay Davis at: 510-746-7368 or [email protected].​


*This workgroup is currently dormant due to the implementation of long-term monitoring in North San Francisco Bay*

The Bay RMP Selenium Workgroup was established in 2014 at the direction of the RMP Steering Committee. San Francisco Bay was listed under section 303(d) of the Clean Water Act as impaired for selenium in 1998. The listing was because elevated concentrations found in biota often exceed levels that can cause potential reproductive impacts in white sturgeon and are often higher than levels considered safe for fish and other wildlife species in the estuary. The problem has been somewhat exacerbated by the introduction of the Asian clam (Corbula amurensis) into the Bay in 1986. This non-native clam is a prodigious filter-feeder, and by consuming large quantities of selenium-laden particles this exotic species provides a pathway for biotransformation of a considerable mass of selenium into the benthic food web. The San Francisco Bay Regional Water Quality Control Board developed a Total Maximum Daily Load (TMDL) and implementation plan for selenium in North San Francisco Bay (NSFB). The TMDL is based on attainment of water column and fish tissue target concentrations protective of human health, aquatic life, and wildlife, and was approved by the U.S. Environmental Protection Agency (USEPA) in August 2016. A primary goal of the Selenium Workgroup is to identify leading indicators of change to allow prompt management response to signs of increasing risk of impairment. Currently, selenium is being monitored in water as well as clam and sturgeon tissue in NSFB. Selenium is also a consistent analyte for the RMP's Status and Trend monitoring work. In 2019 the selenium workgroup began a long-term monitoring project in North San Francisco Bay of water, clams, and sturgeon. The clam and water monitoring data provides a continuation of former USGS monitoring (for more information on these efforts see here and here).

The scientific advisory panel for the Bay RMP Selenium Workgroup consists of:

  • Dr. Harry Ohlendorf, CH2M Hill


Lead Scientist: Jay Davis

For more information, please contact Jay Davis at: ph 510-746-7368 or [email protected] 

*This workgroup is currently dormant*

At the request of the Regional Board, the RMP expanded the biological effects portion of the Status and Trends program, which at the time only monitored for aquatic and sediment toxicity. The Exposure and Effects Workgroup (EEWG) was formed with members from SFEI, USGS, AMS, the Regional Board, and other interested stakeholders. One of the purposes of the workgroup was to develop a biological effects pilot study (the Exposure and Effects Pilot Study (EEPS)) that would help address beneficial use management questions developed by the Regional Board. By building on the recommendations of other effects workgroups, reviewing existing literature related to work in the Estuary, and soliciting recommendations from the local scientific community (through a survey) the workgroup designed a five-year plan for addressing biological effects in the Bay.

The RMP’s EEPS evaluated a balanced suite of contaminant exposure and effects indicators that respond to general and specific contamination at the biochemical, cellular, individual, population, and community level. It evaluated contaminant effects and exposure in different media (on the bay floor, in the water column, and in wetlands/estuary margins), and at different spatial scales (site-specific, regionally, and estuary-wide). These initial overarching principles incorporate recommendations of the EEWG.

At the end of the five year pilot study the workgroup was incorporated into the RMP as a permanent workgroup. The EEWG continues to address the biological effects portion of the Status and Trends program and Pilot and Special Studies.

The scientific advisory panel consists of internationally known experts in this field including:

  • Dr. Michael Fry, Fish and Wildlife Service - Hawaii
  • Dr. Harry Ohlendorf, CH2M Hill
  • Dr. Dan Schlenk, University of California – Riverside
  • Dr. Steve Weisberg, Southern California Coastal Water Research Project


Lead Scientists: Jay Davis

For further information, please contact Jay Davis at: ph 510-746-7368 or [email protected].

Sediment is a critical water quality parameter for the Bay. Sediment transport is a major factor in the fate and transport of priority pollutants such as PCBs and mercury.  Suspended sediment concentrations in the water are also important for preventing large algae blooms despite high nutrient concentrations.

The RMP has been studying sediment since the Program began in 1993. In recent years, sea level rise has heightened the interest in sediment supply to the Bay. The mass balance of sediment in the Bay is a critical factor for marshes and other shoreline habitats to be able to withstand the rising seas. As the San Francisco Bay Restoration Authority decides how to spend $500 million for habitat restoration, it is critical to know how much sediment will be available and where.

In 2018, the RMP created a new Sediment Workgroup to bring together key stakeholders and scientists studying this issue and to prioritize science studies to inform management decisions. There are currently no scientific advisors for the Bay RMP Sediment Strategy Workgroup.

The scientific advisory panel for the Bay RMP Sediment Workgroup consists of internationally respected experts:

  • Dave Schoellhammer, USGS
  • Dr. Pat Wiberg, University of Virginia
Lead Scientist: Scott Dusterhoff
For more information, please contact Scott Dusterhoff at: ph 510-746-7350 or [email protected].

Microplastics are tiny bits of plastic smaller than five millimeters. Their small size exempts them from most current regulations, but makes them difficult to filter out or remove once they are in aquatic ecosystems. Microplastics enter the environment through human use of plastic products. Plastic doesn’t decay – it just breaks down into smaller and smaller pieces. Synthetic clothing and textiles, disposable plastic items like plastic bags and polystyrene foam packaging, tires wearing down as they are driven over roads, and littered cigarette butts can all contribute to microplastic pollution. These tiny bits of plastic may be harmful to aquatic life. Animals may breathe microplastics in via their gills or mistake microplastics for food, and these tiny plastic bits can have toxic effects. Exposure to microplastics also means exposure to the chemical pollutants within the plastics, most of which are emerging contaminants. Because microplastics can be made of many different types of plastics with many different chemistries, scientists are still working to understand the many ways they may affect aquatic organisms and human health.

Our research in the San Francisco Bay has generated a first-of-its-kind, comprehensive regional study of microplastic pollution of a major urban estuary and adjacent ocean environment, making SFEI a world leader in the science of understanding microplastic pollution. As policymakers and water quality managers become more interested in microplastics and their risks to aquatic ecosystems, SFEI science data and conceptual modeling is providing insights that inform local, state, and national decisions to protect the environment.  


Lead Scientists: Diana Lin, Ph.D

For further information, visit www.sfei.org/projects/microplastics or please contact Diana Lin at: 510-746-7385 or [email protected].



This archive contains important documents relating to the establishment and development of the RMP.   


Laying the Foundations: Establishing the RMP


Carlin and Mumley. 1990. San Francisco Estuary Monitoring Program: Working Paper #1.  San Francisco Bay Water Board Resolution No. 92-043 (April 1992): Implementation of the Regional Monitoring Plan within the San Francisco Bay Region 13267 Letter (June 1992) from Water Board to Dischargers: Implementation of a Regional Monitoring Program for the San Francisco Estuary Memorandum of Understanding Between the Water Board and AHI Concerning Implementation of the RMP (1992)


Early RMP Reports

Flegal et al. 1991. Trace Element Cycles in the San Francisco Bay Estuary: Results from a Preliminary Study in 1989-1990 Taberski et al. 1992. San Francisco Bay Pilot Regional Monitoring Program 1991-1992: Summary Progress Report.

SFEI. 1994. 1993 Annual Report: San Francisco Estuary Regional Monitoring Program for Trace Substances.

The first RMP Annual Report

SFBRWQCB. 1995. Contaminant Levels in Fish Tissue from San Francisco Bay.

First report on contaminants in fish tissue, conducted in 1994 under the Bay Protection and Toxic Cleanup Program



Johnston. 1995. Regional Monitoring Program Update.

An account of the formation and status of the RMP included in the first edition of the RMP newsletter Regional Monitoring News

Regional Monitoring News Article. 2004. Founder Steve Ritchie Looks Back at Ten Years of the Regional Monitoring Program.

Excerpts from Steve Ritchie's presentation at the 2003 Annual Meeting celebrating the 10th anniversary of the Program


Meadows. 2013. Celebrating 20 Years of Monitoring San Francisco Bay. 

An insert to Estuary News written by Robin Meadows on the occasion of the 20th Anniversary of the Program 

Davis. 2017.  The 25th Anniversary of the RMP

A review of some of the major milestones in the formation and
development of the RMP

The Regional Monitoring Program for Water Quality in San Francisco Bay is an innovative collaboration of the San Francisco Bay Regional Water Quality Control Board, the regulated discharger community, and the San Francisco Estuary Institute. It provides water quality regulators with the information they need to manage the Bay effectively. The RMP produces two types of summary reports: The Pulse of the Bay and the RMP Update. The Pulse focuses on Bay water quality and summarizes information from all sources. The RMP Update has a narrower and specific focus on highlights of RMP activities.


The purpose of the RMP Update is to provide a concise overview of recent RMP activities and findings, and a look ahead to significant products anticipated in the next two years.

The report includes:

  • a brief summary of some of the most noteworthy findings of this multifaceted Program;
  • a description of the management context that guides the Program; and
  • a summary of progress in, and plans for, addressing priority water quality topics.

Click Here for a PDF of the 2021 RMP Update.

To request hard copies of the Update, please fill out this form: https://forms.gle/cNxBSN88GrPp1mQF9

If you have comments or questions please contact Jay Davis ([email protected])

Previous RMP Updates:

RMP Update 2020     RMP Update 2018     RMP Update 2016     RMP Update 2014     RMP Update 2012

Find an interactive, eBook version of the 2014 RMP Update here


Projects Related to the Regional Monitoring Program for Water Quality in San Francisco Bay

The Pulse of the Bay

Download the Pulse of the Bay! This report from the Regional Monitoring Program for Water Quality in San Francisco Bay features articles on the four major pathways by which pollutants enter the Bay: municipal wastewater, industrial wastewater, stormwater, and dredging and dredged sediment disposal.  Each article provides a basic introduction to the pathway and discusses the regulatory framework, recent findings, and future challenges.  The report also includes some of the latest highlights from monitoring of important parameters such as nutrients, emerging contaminants, mercury, PCBs, and selenium.    

RMP Update

The Regional Monitoring Program for Water Quality in San Francisco Bay is an innovative collaboration of the San Francisco Bay Regional Water Quality Control Board, the regulated discharger community, and the San Francisco Estuary Institute. It provides water quality regulators with the information they need to manage the Bay effectively. The RMP produces two types of summary reports: The Pulse of the Bay and the RMP Update. The Pulse focuses on Bay water quality and summarizes information from all sources.

Contaminant Data Download and Display (CD3)

Contaminant Data Display and Download Tool or CD3  is an innovative visualization tool for accessing water quality data for the San Francisco Bay-Delta and northern montane regions. It is the primary tool for accessing and downloading the San Francisco Bay Regional Monitoring Program’s (RMP) long-term dataset and other project data stored in SFEI's Regional Data Center (RDC).

Contaminants of Emerging Concern Strategy

More than 100,000 chemicals have been registered or approved for commercial use in the US. For many of these chemicals, major information gaps limit evaluations of their potential risks, and environmental monitoring of these chemicals has not been required by regulatory agencies. Nevertheless, researchers and government agencies have begun to collect occurrence, fate, and toxicity data for a number of these chemicals.

Archive Sample Tool

The Archive Sample Tool provides a web interface that SFEI researchers can use to browse the RMP archives when considering using archive material for a study. The RMP has been collecting archive samples during each sampling event for sediment, bivalve, fish and birds since the early 1990's. These samples are available to SFEI researchers with RMP Program Manager approval, and can be requested directly from the tool. 

A Broad Scan of Bay Contaminants: Non-targeted Analysis of Bay Wildlife

A cutting edge analysis identifies low levels of five unmonitored compounds in wildlife of San Francisco Bay. Bay mussel and harbor seal samples were tested for previously unmonitored contaminants using a non-targeted analysis that screens mainly for long-lived, fat-soluble, chlorine and bromine-rich chemicals. The samples contained five contaminants not previously identified in Bay wildlife, and for which toxicity is largely unknown. Most of the Bay chemical contamination was from high priority contaminants that the RMP already monitors, or closely related compounds.

Publications related to the Regional Monitoring Program for Water Quality in San Francisco Bay

The Institute has collectively produced more than 1300 reports, articles, and other publications over the course of its 24-year existence. The following list represents those publications associated with this individual program and its focus areas.

Year of Publication: 2022

Foley MM. 2022 RMP Multi-Year Plan. Richmond, California: San Francisco Estuary Institute; 2022 . Report No.: 1058.  (4.32 MB)
Foley MM. 2022 RMP Multi-Year Plan. Richmond, California: San Francisco Estuary Institute; 2022 . Report No.: 1058.  (4.32 MB)
Moran K, Askevold R. Microplastics from Tire Particles in San Francisco Bay Factsheet. Richmond, CA: San Francisco Estuary Institute; 2022.  (1.38 MB)
Jones C, Davis J, Yee D. Strategy for In-Bay Fate Modeling to Support Contaminant and Sediment Management in San Francisco Bay. Richmond, California: San Francisco Estuary Institute; 2022 . Report No.: 1090.  (2.81 MB)

Year of Publication: 2021

Yee D. 2019 RMP Data Quality Assurance Report. Richmond, CA: San Francisco Estuary Institute; 2021 .  (426.68 KB)
2020-21 RMP North Bay Selenium Study. Richmond, CA: San Francisco Estuary Institute; 2021 . Report No.: 1052.  (7.65 MB)
2020 Bay Margins Sediment Study Cruise Plan. Richmond, California: San Francisco Estuary Institute; 2021 . Report No.: 1073.  (1 MB)
Yee D, Wong A, Weaver M. 2021 Quality Assurance Program Plan for the Regional Monitoring Program for Water Quality in San Francisco Bay. Richmond, California: San Francisco Estuary Institute; 2021 . Report No.: 1048.  (4.63 MB)

Where Our Regional Monitoring Program for Water Quality in San Francisco Bay Works