Our Program and Focus Areas

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

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 the Annual Monitoring Results which document the activities of the program each year, a summary report (Pulse of The Bay), technical reports that document specific studies and synthesize information from diverse sources, and 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

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. Roger Bannerman, USGS, Wisconsin DNR
  • Dr. Michael Stenstrom, University of California – Los Angeles
  • Dr. Kelly Moran, TDC Environmental, LLC


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 the Bay. Emerging contaminants are not currently regulated or commonly monitored, yet may pose significant ecological 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 strategy 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 targeted and broadscan (non-targeted) techniques has identified four emerging contaminants or classes of moderate concern for the Bay:

  • PFOS, a stain and water repellent
  • PFOA and related long-chain perfluorocarboxylates, previously used in fire-fighting foams and to make non-stick coatings
  • Fipronil, an insecticide
  • Alkylphenols and alkylphenol ethoxylates, surfactant ingredients in detergents and many other products

PFOS, PFOA, and other poly- and perfluoroalkyl substances (PFAS) are a particular focus of the RMP, and the subject of a recently completed synthesis and strategy document. Flame retardants known as PBDEs were once moderate concerns for the Bay, but bans and phase-outs reduced contamination to levels of low concern. Many other contaminants have been monitored in the Bay and found to be of low concern as well. A multitude of emerging contaminants fall into a final category of possible concern, where uncertainty in our knowledge of toxicity prevents an evaluation of risk. See the RMP's CEC Strategy (2017 Revision), the 2018 Strategy Update, the 2013 Pulse of the Bay and other Bay RMP resources on emerging contaminants for more information.

The scientific advisory panel for the Bay RMP Emerging Contaminants Workgroup (ECWG) consists of internationally respected experts:

  • Dr. Bill Arnold, University of Minnesota
  • Dr. Miriam Diamond, University of Toronto
  • Dr. Lee Ferguson, Duke University
  • Dr. Kelly Moran, TDC Environmental, LLC
  • Dr. Derek Muir, Environment and Climate Change Canada
  • Dr. Heather Stapleton, Duke University

Lead Scientist: Rebecca Sutton

For further information, please contact Rebecca Sutton at: ph 510-746-7388 or [email protected]

Events and Meeting Materials

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 (2019-2020) 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].​


The first Selenium Strategy Team meeting will be held at SFEI on Tuesday, April 22 from 10 am to 2 pm.

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

  • Dr. Harry Ohlendorf, CH2M Hill


Lead Scientist: Jennifer Sun

For more information, please contact Jennifer Sun at: ph 510-746-7393 or [email protected].

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: Meg Sedlak and 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.

Lead Scientist: Scott Dusterhoff
For more information, please contact Scott Dusterhoff at: ph 510-746-7350 or [email protected].

Findings from a screening-level RMP study of microplastic pollution in our Bay show widespread contamination at levels greater than other U.S. water bodies with high levels of urban development, the Great Lakes and Chesapeake Bay. Wildlife consume microplastic particles; ingestion can lead to physical harm, and can expose aquatic organisms to chemical pollutants in the plastic.

In 2016, the RMP established a Microplastic Workgroup to aid in development of a monitoring strategy and guide further study of this contamination. The scientific advisory panel for the Workgroup includes internationally respected experts:

  • Anna-Marie Cook, USEPA
  • Kara Lavender Law, Sea Education Association, Inc.
  • Chelsea Rochman, University of Toronto

Lead Scientists: Meg Sedlak and Rebecca Sutton

For further information, please contact Meg Sedlak at: ph 510-746-7311 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


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

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

Historical Ecology and Landscape Change in the Central Laguna de Santa Rosa

This study synthesizes a diverse array of data to examine the ecological patterns, ecosystem functions, and hydrology that characterized a central portion of the Laguna de Santa Rosa during the mid-19th century, and to analyze landscape changes over the past 150 years. The primary purpose of this study was to help guide restoration actions and other measures aimed at reducing nutrient loads within this portion of the Laguna de Santa Rosa watershed.

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. 

PBDEs in San Francisco Bay: A Summary Report

Polybrominated diphenyl ethers (PBDEs) are a group of flame retardant additives used in thermoplastics, polyurethane foam, and textiles. These diphenyl ethers possess one to ten bromine atoms; although 209 congeners are possible, only some of these are manufactured or result as degradation products. The three commercial mixtures of PBDEs, each named for the bromination level of its dominant components, are "PentaBDE," "OctaBDE," and "DecaBDE."

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.

Annual Monitoring Report

The San Francisco Estuary Institute has been collecting water, sediment and tissue samples from the San Francisco Bay and tributaries since 1993. These samples are analyzed for ancillary parameters, trace metals and trace organics. Each year a summary of the year's sampling events is published in the Regional Monitoring Program’s Annual Monitoring Results. The results and associated graphics can be accessed using the Contaminant Data Display & Download (CD3) tool. 

Small Tributaries Loading Strategy

The Small Tributaries Loading Strategy (STLS) is overseen by the Sources, Pathways, and Loadings Workgroup. It 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).

RMP eUpdate Newsletter

Sign up for the RMP eUpdate Newsletter and keep up to date on the latest from the San Francisco Bay Regional Monitoring Program (RMP) for Water Quality.

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.
Top Publications
Trowbridge P. Status & Trends Monitoring Design: 2018 Update. Richmond, CA: San Francisco Estuary Institute ; 2018 .  (1.13 MB)
Trowbridge P. 2018 RMP Detailed Workplan and Budget. Richmond, CA: San Francisco Estuary Institute ; 2017 .  (390.05 KB)
Trowbridge P. Charter: Regional Monitoring Program for Water Quality in San Francisco Bay. Richmond, CA: San Francisco Estuary Institute ; 2017 . Report No.: 844.  (1.68 MB)

Year of Publication: 2019

Foley M. 2019 Bay RMP Multi-Year Plan. Richmond, CA: San Francisco Estuary Institute; 2019 . Report No.: 940.  (3.16 MB)
Yee D, Wong A. Evaluation of PCB Concentrations, Masses, and Movement from Dredged Areas in San Francisco Bay. Richmond, CA: San Francisco Estuary Institute; 2019 . Report No.: 938.  (876.18 KB)
Sutton R, Xie Y, Moran KD, Teerlink J. Occurrence and Sources of Pesticides to Urban Wastewater and the Environment. In Pesticides in Surface Water: Monitoring, Modeling, Risk Assessment, and Management [Internet]. Washington, DC: American Chemical Society; 2019. pp. 63-88. https://pubs.acs.org/doi/abs/10.1021/bk-2019-1308.ch005
Gilbreath A, Hunt J, Mckee L. Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015-2018. Richmond, CA: San Francisco Estuary Institute; 2019 . Report No.: 942.  (3.37 MB)
Wu J, McKee L. Regional Watershed Modeling and Trends Implementation Plan. Richmond, CA: San Francisco Estuary Institute; 2019 . Report No.: 943.  (2.25 MB)

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