Our Program and Focus Areas

The Regional Monitoring Program (RMP) is SFEI’s largest program and monitors contamination in the Estuary. It provides water quality regulators with information they need to manage the Estuary 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 the RMP is based on sound science. 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 products and links to other sources of information about water quality in San Francisco Bay.

Charter: Regional Monitoring Program for 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. 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 lester@sfei.org.

Events and Meeting Materials

The Bay RMP fills critical science needs to assist managers in their goals of reducing harmful emerging contaminants in the Bay. Emerging contaminants are not currently regulated, 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 has identified four emerging contaminants of moderate concern for the Bay:

  • PFOS, a stain and water repellent
  • Fipronil, an insecticide
  • Nonylphenols and nonylphenol ethoxylates, detergent ingredients
  • PBDEs, flame retardants

Many more have been monitored in the Bay and found to be of low concern, while a multitude of emerging contaminants fall into a final category of possible concern, where knowledge of occurrence or toxicity is insufficient. See 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 Contaminant Workgroup (ECWG) consists of internationally respected experts:

  • Dr. Lee Ferguson, Duke University
  • Dr. Jennifer Field, Oregon State University
  • Dr. Phil Gschwend, Massachusetts Institute of Technology
  • Dr. Derek Muir, Environment Canada
  • Dr. David Sedlak, University of California - Berkeley
  • Dr. Kelly Moran, TDC Environmental, LLC

Lead Scientist: Rebecca Sutton

For further information, please contact Rebecca Sutton at: ph 510-746-7388 or rebeccas@sfei.org

Events and Meeting Materials

PCBs are a pollutant of high concern in San Francisco Bay. The PCB strategy ensures that the RMP is providing the information most urgently needed by managers to 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. Because the PCB strategy integrates across workgroup areas, special studies designed to address the PCB strategy are reviewed by the most relevant workgroup, such as the EEWG or the CFWG. Studies under the PCB Strategy began in 2010. A PCB synthesis in 2014 will set the stage for a multi-year study plan.

The scientific advisory panel for the Bay RMP PCBs 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 jay@sfei.org.



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 Jennifers@sfei.org.

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 jay@sfei.org.

Events and Meeting Materials

San Francisco 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. RMP studies of contaminants in Bay sport fish conducted every three years since 1994 have found that dioxin concentrations have remained relatively unchanged over this time period and in some species, continue to exceed screening values for human consumption. Our understanding of dioxin in the Bay is extremely limited however and improving this is a necessary first step in the process to reduce concentrations in Bay fish and resultant health risks to fish-eating humans and wildlife. The dioxin strategy ensures that the RMP is providing information that is of highest value and most urgently needed by managers for development of a dioxin TMDL. The upcoming management decisions include reissuing permit requirements for dioxins, reviewing 303(d) listings, and establishing a TMDL development plan (2013-2014). Dioxin Strategy studies began in 2008, with a multi-year plan extending through 2012. Because the dioxin strategy integrates across workgroup areas, special studies designed to address the dioxin strategy are reviewed by the most relevant workgroup, such as the EEWG or the CFWG. Synthesis activities are planned for 2013 and 2014 after the data from the earlier studies are available.

The scientific advisory panel for the Bay RMP Dioxins Strategy Workgroup consists of:
Dr. Frank Gobas, Simon Fraser University
Lead Scientist: Don Yee
For more information, please contact Don Yee at: ph 510-746-7369 or donald@sfei.org.

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

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).

The Pulse of the Bay

Download this year’s Pulse of the Bay! The newly released report from the Regional Monitoring Program for Water Quality in San Francisco Bay summarizes the present state of Bay water quality and looks into the crystal ball at what the condition of Bay water might be 50 years from now.

The Pulse is a companion to the State of the Estuary Report and examines whether Estuary waters are clean enough to be safe for fishing, for swimming, and to provide healthy habitat for aquatic life.

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. 

RMP Annual Meetings

The RMP hosts the RMP Annual Meeting in early fall, which unites RMP stakeholders to discuss current RMP projects and highlight one area of research, such as stormwater, sediment, mercury, or emerging contaminants. The 2015 RMP Annual Meeting will be part of the 12th Biennial State of the Estuary Conference.

Bay RMP in Estuary News

Estuary News, a publication of the San Francisco Estuary Partnership, has been reporting San Francisco Bay, Delta and watershed news for over 25 years, and won an award for excellence in 2011. This 12-page mini-magazine comes out four times a year on paper and in PDF. It covers everything from restoration and conservation to the water wars, and offers insider information on the latest debates, regulations and science on contaminants, endangered species and invasives.

The Bay RMP contributes to the production of Estuary News, and many articles feature the latest Bay RMP findings.

Annual Monitoring Results

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).

Copper Site Specific Objective 3-year Rolling Averages

As part of the copper site-specific objective, NPDES dischargers are required to calculate annually the three-year rolling average of dissolved copper concentrations in water in each segment of the Bay, based on RMP data.a This table presents the segment average and corresponding trigger levels in the Basin Plan.

Sport Fish

Fish from San Francisco Bay contain concentrations of mercury, PCBs, and other chemical contaminants that are above thresholds of concern for human health. This problem was first documented in 1994 when the San Francisco Bay Regional Water Quality Control Board (SFBRWQCB) performed a pilot study to measure contaminant concentrations in Bay sport fish (Fairey et al. 1997).

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."

Publications Issued by 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: 2015

Institute SFrancisco. 2013-2014 Annual Monitoring Results. Richmond, CA: San Francisco Estuary Institute; 2015 . 2013-2014_AMR_Final.pdf (2.86 MB)
2015 RMP Detailed Workplan. Richmond, CA: San Francisco Estuary Institute; 2015 . 2015 RMP Detailed Workplan.pdf (546.26 KB)
2015 RMP Multi-Year Plan. Richmond, CA: San Francisco Estuary Institute; 2015 . 2015 RMP Multi-Year Plan.pdf (2.22 MB)
2015 RMP Program Plan. Richmond, CA: San Francisco Estuary Institute; 2015 . 2015 RMP Program Plan.pdf (414.17 KB)
Sutton R, Kucklick J. A Broad Scan of Bay Contaminants. Richmond, CA: San Francisco Estuary Institute; 2015 . SFEI&ASC NIST factsheet web.pdf (1.34 MB)

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