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: 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.

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 innovative science and modeling, and in collaborative partnership with with the San Francisco Estuary Partnership (SFEP), the Regional Water Quality Control Board (Regional Board) and municipalities, we tackle hard questions regarding Green Infrastructure performance, planning, and management, such as:

• How does Green Infrastructure perform in reducing runoff and urban pollutants?
• Where can Green Infrastructure be implemented most cost effectively in our urban landscape?
• How much will it cost and what benefits can we get for our investment?
• How do we track green features that are implemented over time?
• How do we account for the multi-benefits of Green Infrastructure?


GreenPlan-IT is a versatile open-source toolset designed to assist municipal managers with strategic placement of Green Infrastructure and watershed master planning. The toolset helps municipalities to meet their stormwater permit requirements and other programmatic needs and facilitates compliance and effectiveness reporting through innovative data management and modeling techniques. The GreenPlan-IT tool allows municipalities to evaluate multiple management alternatives using green infrastructure to address stormwater issues in urban watersheds. Quantitatively-derived watershed master plans can be developed with GreenPlan-IT to guide future green infrastructure implementation. A wealth of information about the project, including how to download and use the tool, can be found on the GreenPlan-IT website.


SFEI uses field monitoring to derive a better understanding of how green infrastructure functions in our semi-arid climate and for our regional-specific concerns.  Field studies focus on both hydrologic changes and/or water quality changes as the result of green infrastructure.