Our Program and Focus Areas

Water Quality Science Informing Stewardship

SFEI’s Clean Water Program is one of the nation’s premier water quality science programs. It anticipates and meets the water quality data needs of policy-makers, resource managers, and the public. It helps the public, regulators, and those who discharge into our waters create more effective policies to ensure the health of our waters. The Clean Water Program consists of several programs and initiatives:

  • The Regional Monitoring Program for Water Quality in San Francisco Bay (Bay RMP) — Now in its 22nd year, the RMP is the flagship of the Clean Water Program. The RMP is a model program to present decision makers with the best available science on pollution in San Francisco Bay. The RMP combines high quality science, forward planning, public forums, and the delivery of clear and actionable data to watershed managers and the public.
  • SFEI has helped develop the Delta RMP to inform better policy-making for Delta water quality, and is about to begin the first year of monitoring. As with its Bay-focused predecessor, the Delta RMP will provide the science to drive lower-cost, more efficient and effective regulations. This science will benefit the Delta’s many users, from farmers to fisherman, boaters to residents.
  • SFEI is the scientific lead for the San Francisco Bay Nutrient Strategy, to address the most complex and costly issue confronting the wastewater treatment community since the Clean Water Act mandated secondary treatment 40 years ago.
  • Our Green Chemistry research fills critical needs of agencies involved in efforts to prevent pollution by advising manufacturers about safer options.
  • The Green Infrastructure initiative provides scientific support and innovative tools for long-term planning of water infrastructure upgrades to achieve green alternatives, improved water quality, and sustainability.

For more information on the SFEI Clean Water Program, please contact Program Directors Jay Davis, Ph.D. and David Senn, Ph.D.


The Bay Regional Monitoring Program (RMP) provides water quality regulators and policy-makers with information they 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. The Program was established in 1993, and has an annual budget of $3.5 million.


RMP Manager: Melissa Foley   Lead Scientist: Jay Davis


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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.

Pollutants that accumulate in the food web (or “bioaccumulate”) are impairing the health of aquatic ecosystems throughout California. Methylmercury bioaccumulation is a particularly widespread and severe problem, and poses a serious threat to human and wildlife health across the state. Monitoring information will provide an essential foundation for control plans and exposure reduction plans to remedy bioaccumulation problems in California water bodies. In addition, effective communication of this information to the public is imperative to enable fish consumers to reduce their exposure to pollutants.

However, California still lacks the comprehensive monitoring, assessment, and communication needed to adequately support management of bioaccumulative pollutants in California water bodies. There are multiple problems with the status quo:

  • insufficient information on spatial extent and long-term trends, high priority topics such as contaminants of emerging concern (CECs) and biotoxins, and the relative importance of different sources and environmental factors that drive bioaccumulation;
  • inefficiencies due to a lack of coordination between agencies, and between agencies and regulated entities;
  • a need for pilot scale actions to reduce bioaccumulation accompanied by refinement of monitoring tools to track the effectiveness of the actions;
  • safe eating guidelines are needed for many additional water bodies, but the current pace of development is slow due to funding limitations,
  • a need for optimizing the effectiveness of communication to the public in support of exposure reduction, and
  • insufficient access to data and information for regulators, scientists, and the public.

Efficient use of the limited funds available for monitoring, assessment, and communication is of paramount importance. This efficiency can be achieved through close coordination of programs and thoughtful strategic planning. California needs a central entity with the responsibility and authority to convene a forum to attain the degree of coordination and cooperation that is required to address the bioaccumulation problem. The Bioaccumulation Oversight Group (BOG) has been established as a work group of the California Water Quality Monitoring Council to fulfill this role. A Strategy for Coordinated Monitoring, Assessment, and Communication of Information on Bioaccumulation in Aquatic Ecosystems in California has been prepared by the BOG to outline steps that should be taken to improve bioaccumulation monitoring, assessment, and communication in California.

SFEI acts as the scientific lead for developing and implementing the Bay’s Nutrient Management Strategy. In this role, SFEI staff work with teams of regional scientists to develop the necessary scientific understanding to allow regulators and stakeholders to make informed decisions about i) whether the Bay is trending toward nutrient-related impairment; ii) what nutrient reductions are needed to mitigate or prevent impairment; and iii) sub-regional and regional approaches that achieve necessary reductions and yield the highest ratios of overall benefits to cost.


San Francisco Bay receives high anthropogenic loads of the nutrients nitrogen and phosphorous - higher than many other US estuaries that experience nutrient-related water quality impairments such as excessive algal blooms, low dissolved oxygen and fish kills, and blooms of toxin-producing algae. Until recently, the Bay was considered to have innate strong resistance to high nutrients. However, recent observations suggest that the Bay is experiencing a “regime shift” toward higher sensitivity to nutrients. The Bay’s true trajectory is cloaked in uncertainty. One plausible scenario is that the Bay’s current level of resistance will be maintained and no further degradation will occur. Another equally plausible scenario is that the Bay’s resistance to nutrients will continue to decline until moderate to severe impairment occurs in some subembayments.

Treated wastewater from the Bay Area’s 42 publicly owned treatment works (POTWs) is a major nutrient source Bay-wide. Waters entering the Bay from the heavily-farmed Central Valley act as another large nutrient source that disproportionately influences the northern Bay. Upgrading POTWs to substantially decrease nutrient loads will come at enormous public expense: $2-10 billion. That expense is undoubtedly justified if nutrients are indeed causing (or will eventually lead to) impairment, and if reducing POTW loads will mitigate or prevent that impairment. However, the scientific foundation needed to explore those issues needs to be developed.

Bay Area POTWs describe nutrients as the most complex and costly issue confronting them since the Clean Water Act mandated secondary treatment 40 years ago. Regulators and dischargers are highly engaged and seeking alignment. In that sense, nutrients also represent an enormous opportunity: a catalyst for sub-regional and regional water and wastewater planning to achieve multiple long-term objectives.

Watershed Loadings conducts management- and policy-related scientific research on the physical, chemical, and biological function of the watersheds and urban catchment of San Francisco Bay. Areas of research include geomorphology, hydrology and sediment transport, contaminant source investigation, contaminant hydrology, testing the effectiveness of Best Management Practices (BMPs), and modeling loads and BMP selection alternatives. Research projects are carried out through collaborations with government managers and scientists, the private sector, and academia.

Program Overview

The Regional Watershed Program conducts management- and policy-related scientific research on the physical, chemical, and biological function of the watersheds of San Francisco Bay and the maintenance of function though the application of best Management Practices. Areas of research include geomorphology, hydrology and sediment transport, contaminant hydrology, modeling, and testing the effectiveness of management measures. Research projects are carried out through collaborations with government managers and scientists, the private sector, and academia. Watersheds of the Bay Area and Central Valley are evolving in response to natural factors such as decadal-scale climatic variation and anthropogenic factors such as climate change, redevelopment and land use conversion, impervious cover, and agricultural land management. These “pressures” result in local and regional scale hydro-modification, erosion, degraded water quality, stream habitat change, and broad scale landscape change. Although system “states” can be considered separately, in reality they are highly interconnected. In an effort to counteract these pressures, managers seek to control flow using reservoirs, flood conveyance channels, stream hardening, and impervious surface disconnection, improve water quality through urban and agricultural BMPs, and preserve habitats and species through remnant conservation, predator control, habitat restoration, and sustainable land management. The challenge facing the scientific and management communities and public of the Bay Area is to assist and encourage the development of integrated management techniques at a variety of system scales across the full range of management paradigms that are consistent with the most recent scientific understanding of integrated pressure-state.

Program Objectives

  • Develop a regional picture of watershed condition and downstream effects through a solid foundation of literature review, empirical data collection and interpretation, and peer-review.
  • Assist local environmental managers and other scientists to understand the way watersheds function locally and regionally in the Bay Area through the development innovative projects that address current needs.
  • Be adaptive and aware of changing management needs.
  • Communicate results using a variety of media including technical reports, presentations, workgroups, newspaper and magazine articles, scientific journals and conferences.

Program Staff

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].


Projects Related to the Clean Water Program

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.


Green infrastructure (GI), such as permeable pavement, rain gardens, tree-well planters, or bioswales, can be used as cost-effective, resilient approaches to managing stormwater at its source while delivering environmental, social, and economic benefits for your community. GreenPlan-IT is a versatile open-source toolset that helps aid municipalities with their efforts to plan and evaluate the placement of green infrastructure in the landscape and track the effectiveness of these installations in reducing stormwater run-off, PCB, and mercury in receiving waters.

Russian River Watershed Projects at the San Francisco Estuary Institute

Our projects in the Russian River Watershed help us to understand our past, understand our present, and envision our future. Learn more about what SFEI is doing in partnership with others to advance our scientific understanding of this valuable landscape.

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).

Satellite Imaging to Detect Cyanobacterial Blooms

Satellite remote sensing will aid the State of California in assessing cyanobacterial bloom threats to animal and human health across the state’s numerous large lakes. 

Microplastic Pollution in San Francisco Bay and Adjacent Marine Sanctuaries

Plastic pollution is gaining global recognition as a threat to the resilience and productivity of ocean ecosystems. However, we are only just beginning to understand the scope and impacts of microplastic particles (less than 5 mm) on coastal and ocean resources, and the San Francisco Bay Area is no exception. A preliminary study of nine water sites in San Francisco Bay, published in 2016, showed greater levels of microplastics than the Great Lakes or Chesapeake 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.    

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.

SF Bay Nutrients Visualization Tool

This visualization tool facilitates intuitive comparison of continuous data from around the Bay, and across a variety of analytes, to demonstrate the potential for collaborative monitoring across programs.

Safe to Eat Portal

Fish and shellfish are nutritious and good for you to eat. But some fish and shellfish may take in toxic chemicals from the water they live in and the food they eat. Some of these chemicals build up in the fish and shellfish - and in the humans that eat fish and shellfish - over time. Although the chemical levels are usually low, it is a good idea to learn about advisories and monitoring in water bodies where you fish, and for fish or shellfish you eat.

Publications related to the Clean Water Program

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

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)
Foley M. 2021 RMP Multi-Year Plan . Richmond, CA: San Francisco Estuary Institute; 2021 . Report No.: 1027.  (3.5 MB)
Moran K, Miller E, Mendez M, Moore S, Gilbreath A, Sutton R, et al.. A Synthesis of Microplastic Sources and Pathways to Urban Runoff. Richmond, CA: San Francisco Estuary Institute; 2021 . Report No.: 1049.  (9.17 MB)
Buzby N, Davis JA, Sutton R, Miller E, Yee D, Wong A, et al.. Contaminant Concentrations in Sport Fish from San Francisco Bay: 2019. Richmond, CA: San Francisco Estuary Institute; 2021 . Report No.: 1036.  (5.15 MB)
Zi T, Kauhanen P, Whipple A, Mckee L. Green Stormwater Infrastructure Planning-level Analysis for Livermore-Amador Valley. Richmond, Calif.: San Francisco Estuary Institute; 2021 . Report No.: 1063.  (20.75 MB) (12.19 MB)
Gilbreath A, McKee L, Hunt J. Pollutants of Concern Reconnaissance Monitoring Progress Report, Water Years 2015-2020. Richmond, CA: San Francisco Estuary Institute; 2021 . Report No.: 1061.  (3.22 MB)

Where Our Clean Water Program Works