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: Melissa Foley   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.

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.

Hydrology, Green Stormwater Infrastructure, and Watershed Loadings

The goals of Hydrology Focus Area are to

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;
apply modeling tools to assist the development of sound environmental policies at watershed and regional scales; and
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.

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.