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.

Events and Meeting Materials:


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: Phil Trowbridge   Lead Scientist: Jay Davis


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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.

The Delta is California’s water crossroads. It provides two-thirds of Californians - an estimated 25 million people - with water. It irrigates more than 7,000 square miles of agricultural lands. The Delta also supports more than 80% of the state’s commercial salmon fishery, and is home to more than 750 plant and animal species - including 31 species that are threatened or endangered – that, in some cases, are found nowhere else.

Yet at the same time, concerns about degraded water quality and its impact on these beneficial uses are ever- present and serious. For example, degraded water quality has been implicated as one of the possible causes for the decline of native species, along with various other and seemingly interconnected issues facing the Delta, such as water diversions and the loss of habitat. The complexity of the Delta’s challenges has highlighted the importance of comprehensive information on its condition.

The Delta RMP will address this need by better defining water quality issues of regional concern and working to improve the quality and efficiency of water quality monitoring information. Initial priorities are an improved understanding of the spatial and temporal distribution of prioritized water quality constituents (i.e. ancillary parameters, methylmercury, nutrients, pathogens, pesticides, and toxicity) in the Delta, improving the efficiency and usefulness of compliance monitoring and data reporting, and fostering large-scale collaborations. Monitoring is expected to begin in 2015. Building a successful Delta RMP is consistent with SFEI-ASC’s core mission. Building a successful Delta RMP will be a win-win-win for the community, regulators, and the Delta ecosystem, achieved through more efficient monitoring, more comprehensive information, and more effective water quality protection.

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.

Events and Meeting Materials:

The Green Infrastructure initiative helps provide vision and scientific support related to near-term and long-term planning and implementation of water infrastructure upgrades toward green alternatives and improved sustainability. Over the coming years and decades, the Bay Area will face multiple, complex, inter-related, and expensive decisions related to stormwater and wastewater management. These decisions will be motivated by the need to remove contaminants, restore natural services of aquatic ecosystems, increase water reuse, and replace aging infrastructure. In order to maximize benefits and efficiencies, these various efforts need to be considered within a comprehensive, regional planning process that integrates vertically through government, with reasonable analyses of costs, benefits, risks, and future requirements.

Through our Green Infrastructure Initiative, we will work with regional leaders in LID and green chemistry to address the overarching questions: “What should wastewater, stormwater, and water use and reuse/recycling look like in 50 years in the Bay Area? What is necessary? What is feasible?” Under the Green Infrastructure Initiative, Clean Water, Resilient Landscapes, and Environmental Informatics will convene technical advisory groups focused on stormwater, wastewater, and ecosystem restoration. We will work closely with the San Francisco Estuary Partnership (SFEP), the Regional Water Quality Control Board (Regional Board) and municipalities to plan and implement innovative projects focused on different time horizons. Key outputs will include regional and sub-regional analyses of benefits (water quality, flood protection, and habitat conservation) and associated costs, with the goal of formulating an optimal regional Green Infrastructure master plan.

Events and Meeting Materials:

The goals of Hydrology Focus Area are to

  1. develop and maintain modeling tools to incorporate available knowledge into a quantitative framework that can be used to simulate and predict the outcome of alternative approaches and policies;
  2. apply modeling tools to assist the development of sound environmental policies at watershed and regional scales; and
  3. provide data sharing and information access through open source model platforms and model applications.

The SFEI/ASC Strategic Plan calls for improved scientific support and tools to help inform the decisions of environmental planners, managers, and regulators in protecting aquatic ecosystems in the Bay-Delta region and beyond. Watershed-scale hydrologic modeling has emerged as an important scientific research and management tool to understand and address increasingly difficult and interrelated water resources issues. Currently, this powerful tool has not been sufficiently utilized in the region to better support management and decision-making. The Hydrology Focus Area aims to fill this gap in order to fulfill the growing need of stakeholders and government agencies for better tools and quantitative information to manage complex water supply, water quality, flood control, and habitat protection issues.

SFEI acts as the scientific lead for developing and implementing the Bay’s Nutrient 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

Projects Related to the Clean Water Program

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.

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 last year’s Pulse of the Bay! This 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.

Hacienda Avenue Bio-Infiltration Basins

The Hacienda Avenue Green Street Project in Campbell, California, reconstructed 1.4 km of public right of way along W. Hacienda Avenue from Winchester Boulevard to Burrows Road. In collaboration with the City of Campbell and the San Francisco Estuary Partnership, scientists from SFEI installed monitoring equipment in two adjacent basins to measure how the basins infiltrated water over the course of a rainy season. This award-winning project infiltrated 100% of the stormwater flowing into it during the rainy season of 2015-2016.

Microplastic Pollution

The RMP has conducted initial studies of microplastic pollution in San Francisco Bay. 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 pollutants like PCBs that the plastics have absorbed from the surrounding environment.

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, including fish, and the Bay Area is no exception.

San Francisco Bay Fish Project

The San Francisco Bay Fish Project is a two-year project to reduce exposure to harmful chemicals from eating San Francisco Bay fish. This Project is part of the Regional Water Quality Control Board’s strategies to reduce the levels of PCB and mercury in the Bay (these strategies are called Total Maximum Daily Loads, or TMDLs). The Project is intended to improve communication to the public about how to reduce their exposure to PCBs and mercury from consuming San Francisco Bay fish while the Water Board works to reduce the levels of PCBs and mercury in those fish.

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.

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. 


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.

Publications Issued by 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: 2017

RMP. 2017 RMP Detailed Workplan and Budget. Richmond, CA: San Francisco Estuary Institute; 2017 .  (2.27 MB)
RMP. 2017 RMP Multi-Year Plan. Richmond, CA: San Francisco Estuary Institute; 2017 .  (2.14 MB)
Sutton R, Sedlak M. Microplastic Monitoring and Science Strategy for San Francisco Bay. Richmond, Calif.: San Francisco Estuary Institute; 2017 . Report No.: 798.  (17.38 MB)
Wu J, Gilbreath A, McKee LJ. Regional Watershed Spreadsheet Model (RWSM): Year 6 Progress Report. Richmond, CA: San Francisco Estuary Institute; 2017 .  (1.79 MB)
Yee D, Ross J. San Francisco Bay California Toxics Rule Priority Pollutant Ambient Water Monitoring Report. Richmond: San Francisco Estuary Institute; 2017 . Report No.: 814.  (1.92 MB)

Year of Publication: 2016

SFEI. 2015 Annual Monitoring Report. Richmond, CA: San Francisco Estuary Institute; 2016 . Report No.: 775.  (3.28 MB)
Shimabuku I. 2015 Update to Copper Rolling Average. Richmond, CA: San Francisco Estuary Institute ; 2016.  (951.49 KB)
Shimabuku I. 2015 Update to Cyanide Rolling Average. Richmond, CA: San Francisco Estuary Institute ; 2016.  (941.06 KB)
San Francisco Estuary Institute (SFEI). 2016 Regional Monitoring Program Update. Richmond, CA: San Francisco Estuary Institute; 2016 . Report No.: 790.  (6.27 MB)
Davis J, Trowbridge P, Yee D, Franz A. 2016 RMP Bird Egg Monitoring Sampling & Analysis Plan. Richmond, CA: San Francisco Estuary Institute; 2016 .  (227.48 KB)

Where Our Clean Water Program Works