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 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
  • Imidacloprid, neonicotinoid insectiside
  • Organo-phosphate Esters, flame retardants
  • Bisphenols, commonly found in plastic 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 2020 Strategy Update, and the 2019 Pulse of the Bay 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. Dan Villinueve, US EPA
  • Dr. Derek Muir, Environment and Climate Change Canada
  • Dr. Heather Stapleton, Duke University

Green chemistry is a critical tool in efforts to prevent the pollution of our environment. By selecting safer chemicals and processes for making consumer products, we limit contamination that can adversely impact the health of the Bay and other aquatic ecosystems. We can also reduce expensive monitoring, remediation, and management actions.

SFEI provides applied science that policymakers and managers need to make well-informed decisions. Our green chemistry research fills critical needs of state and local agencies involved in the effort to guide manufacturers towards safer choices. A key focus is advising California's unique green chemistry approach, taking shape through the Safer Consumer Products Regulations. Pollution prevention measures informed by SFEI's green chemistry studies play a notable role in supporting and protecting healthy aquatic ecosystems through independent science.

Recent highlights of SFEI’s green chemistry focus area:

  • January 2017: Senior scientist Dr. Rebecca Sutton presents information on key contaminants associated with aquatic impacts to the Department of Toxic Substances Control to inform implementation of the Safer Consumer Products Regulations.
  • January 2017: A letter to Health Canada regarding proposed regulations on the pesticide imidacloprid highlights new findings relevant to spot-on flea control products.
  • January 2016: Dr. Sutton speaks at a California legislative science-policy briefing on ocean and freshwater plastic pollution.
  • May 2015: Dr. Sutton provides testimony to California's Proposition 65 Scientific Advisory Board regarding the reproductive toxicity of bisphenol A. Board members unanimously list bisphenol A as a reproductive toxicant.
  • February 2015: Dr. Sutton presents new data on flame retardants in San Francisco Bay as part of the 2015 Flame Retardants Dilemma symposium.
  • January 2014: Dr. Sutton is appointed to state Green Ribbon Science Panel to inform the implementation of the Safer Consumer Products Regulations. The appointment is renewed in 2017.


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

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

Regional Watershed Spreadsheet Model

The Regional Watershed Spreadsheet Model (RWSM) was developed to estimate average annual regional and sub-regional scale loads for the San Francisco Bay Area. It is part of a class of deterministic empirical models based on the volume-concentration method.

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. 

Flood Control 2.0

Flood Control 2.0 is an ambitious regional effort aimed at helping restore stream and wetland habitats, water quality, and shoreline resilience around San Francisco Bay. The project leverages local resources from several forward-looking flood control agencies to redesign major flood control channels so that they provide both future flood conveyance and ecological benefit under a changing climate. This timely project will develop a set of innovative approaches for bringing environmental benefits and cost-savings to flood protection efforts at the mouths of creeks that drain to San Francisco Bay.

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.

Carlos Street Rain Garden Interpretative Sign

The Carlos Street rain garden in Moss Beach collects and filters stormwater from the street, Post Office parking lot, and adjacent private properties and businesses. By placing small rain gardens in strategic locations, pollution going to local water bodies is reduced, resulting in improved water quality in the Fitzgerald Marine Reserve and designated Area of Special Biological Significance.

Moored Sensor Monitoring Program for Nutrients

The indications of decreased Bay resilience to high nutrient loads have come to the fore at a time when the availability of resources to continue assessing the Bay’s condition is uncertain. The San Francisco Bay Regional Monitoring Program (RMP) has no independent nutrient‐related monitoring program, but instead contributes approximately 20% of the USGS data collection cost. Thus, there is currently an urgent need to lay the groundwork for a locally‐supported, long‐term monitoring program to provide information that is most needed to support management decisions in the Bay.

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: 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)
Zi T, Mckee L, Yee D, Foley M. San Francisco Bay Regional Watershed Modeling Progress Report, Phase 1. Richmond, CA: San Francisco Estuary Institute; 2021 . Report No.: 1038.  (8.84 MB)

Where Our Clean Water Program Works