The Science of Puget Sound Water Quality


Building on the foundation

In developing the forthcoming Puget Sound Partnership Marine Water Quality Implementation Strategy, regional experts identified technical uncertainties and research priorities, including several related to dissolved oxygen and nutrients. The Puget Sound Institute is helping to address some of these priorities with support from King County and municipalities in the Puget Sound Clean Water Alliance. These efforts are intended to build on the discussions and modeling that the Washington State Department of Ecology (Ecology) is leading with the Puget Sound Nutrient Reduction Project.

Puget Sound Institute is collaborating to:

  • Facilitate scientific workshops with regional stakeholders
  • Convene national and international experts in a Model Evaluation Group to share their perspectives from similar efforts
  • Inform decision-making through access to the latest science and tools, including models, outputs, and monitoring data
  • Lead additional technical analysis, including model runs, that complement existing and planned work by others to address scientific questions and uncertainties

Interested in learning more? Have a topic you would like to see explored?
Email Stefano ( and Marielle (

The Challenge

Our region is navigating complex decisions on how best to manage nitrogen, dissolved oxygen, and the potential impacts of eutrophication on the key habitats and species of the Salish Sea. In the face of multiple stressors, including climate change and population growth, it’s even more challenging to evaluate and implement solutions that address a range of water quality priorities that affect orca and salmon recovery. Complex challenges like these require multi-faceted, complementary efforts to solve. Environmental leaders in the region have created a strong foundation to build on, from the Washington State Department of Ecology Puget Sound Nutrient Reduction Project to the Puget Sound Partnership’s forthcoming Marine Water Quality Implementation Strategy1 & 2.

While land-based nitrogen loading to the Salish Sea is estimated to be less than 2% of ocean loadings (Khangaonkar et al. 2018), it is much harder to determine the proportion from human activities that impacts water quality and biological integrity in marine habitats. Continuing to advance modeling is necessary to understand how these nutrients can fuel biological change, and to determine what combination of wastewater and watershed reductions will stop the progression of eutrophic symptoms.

Modeling by the Department of Ecology found that at least half of the anthropogenic nitrogen loading to the Sound is from wastewater treatment plants (Ahmed et al. 2021; Mohamedali et al. 2011). Currently, most wastewater treatment plants in the region are not designed to remove nitrogen3. Based on initial estimates, municipalities in the region will likely need to invest billions to upgrade wastewater treatment plants to remove nitrogen. As a significant investment that will shape our region’s future for decades, there are naturally different perspectives on how best to manage these water quality challenges.

Models help us explore the technical uncertainties in what we understand about the system, and in the management scenarios considered. Puget Sound Institute (PSI) plans to build on these ongoing regional efforts to help address technical uncertainties and to advance modeling tools to improve the understanding of nutrients and broader water quality challenges in the Salish Sea.

Why Puget Sound Institute?

Since its founding in 2010, Puget Sound Institute has advanced our scientific understanding of Puget Sound through synthesis, original research, and communication in support of state and federal agencies and other organizations.

Puget Sound Institute supports Puget Sound recovery and the development of Implementation Strategies, including the Marine Water Quality Implementation Strategy, primarily by:

  • Documenting key technical uncertainties that are identified as limiting either the development or the prioritization and optimization, of resulting strategies
  • Detailing the current science and policy frameworks available to implement the strategies through both the State of Knowledge (SoK) and the Base Program Analysis (BPA) reports.

While the Marine Water Quality Implementation Strategy is currently undergoing peer review, the Science Panel reviewed the technical uncertainties in 20211 and asked Puget Sound Institute to facilitate collaboration to reduce some of the uncertainties through analysis and modeling.2 In 2020, Puget Sound Institute (PSI) also helped launch the Salish Sea Modeling Center. The Salish Sea Model itself is an integral tool used by the state (among others) to understand the physical, biogeochemical and key biological process dynamics in the Salish Sea, and to investigate how different management actions can potentially improve environmental health. Puget Sound Institute is therefore uniquely positioned to advance and expand access to modeling, and facilitate workshops to help address the technical uncertainties prioritized by regional stakeholders.

As always, we are committed to transparent, collaborative science, and will continue to facilitate shared approaches to analysis and model outputs.

Scientific workshops

We are facilitating scientific workshops for utilities, environmental community-based organizations, scientists, agencies, and the tribes to explore and address some of the technical uncertainties related to nutrient impacts and water quality. These workshops build on previous discussions such as Ecology’s Nutrient Forum and on the uncertainties in the forthcoming Marine Water Quality Implementation Strategy to dig deeper into identified challenges such as the interannual variability of ocean influences on the Salish Sea.

We appreciate how generous numerous monitoring experts, modelers, managers, and researchers have been with their time as we collaborate on designing the workshops. Good science benefits from robust discussion and a range of perspectives, so we look forward to engaging with more experts and are happy to connect individually.

If you have ideas on how our region can start to address these technical uncertainties, we’d love to connect! Please also feel free to share relevant papers, monitoring data, or experts that you think would be helpful. In particular, we recognize we need to more effectively engage and build relationships with environmental community-based organizations, tribes, as well as scientists in British Columbia.

Email Stefano ( and Marielle (

Upcoming workshops: TBD

Summary of prior workshops

Thank you to everyone who’s contributed to energizing discussions at the workshops thus far. Over 440 people have joined us, ranging from researchers at universities to scientists at utilities and agencies to modelers from across the border to leaders at environmental community-based organizations.

You can find a recap for each workshop below, which includes a summary, highlight video, full recording, chat, and slides.

You can also explore all the workshop videos on our playlist.
Kickoff: The science of Puget Sound water quality 7.26.22

Thank you to everyone who contributed to an energizing discussion on The Science of Puget Sound Water Quality on July 26, 2022. You can review the summary or watch all of the videos from the workshop on this playlist. Additionally, you can access the materials for each section directly, below. The chat is also available.

  • Intro & Keynote from Dr. Martha Sutula
    Martha Sutula, Southern California Coastal Water Research Project
  • Dissolved Oxygen Impacts on the Biological Integrity of Key Habitats and Species
    Martha Sutula, Southern California Coastal Water Research Project
  • Change in Interannual Variability of Rivers and Ocean Impact
    Parker MacCready, Live Ocean, University of Washington
    Tarang Khangaonkar, Salish Sea Modeling Center, University of Washington
  • Phytoplankton and Primary Production
    Julia Bos, Phytoplankton and Primary Production Vital Sign Co-lead
  • Watershed Modeling
    Bob McKane, Environmental Protection Agency
Tools to evaluate water quality 9.29.22

We enjoyed a thoughtful discussion with Stephanie Jaeger, Gordon Holtgrieve, and a range of experts about Tools to Evaluate Water Quality on September 29, 2022. The discussion highlighted analyses from long-term monitoring, isotopic studies, and modeling that help us better understand water quality and potential eutrophication impacts, particularly in embayments. The Salish Sea Model already calculates additional parameters beyond dissolved oxygen for each cell and layer, daily. So please don’t hesitate to reach out if you’d like access to or analyses of these existing parameters (Stefano Mazzilli and Marielle Larson


Biological integrity of key species and habitats 10.6.22

Thank you to everyone who joined us early on October 6, 2022 to expore the Biological Integrity of Key Species and Habitats. Dr. Jacob Carstensen of the Baltic Nest Institute shared what can be learned from managing oxygen problems in the Baltic Sea. Then Dr. Tim Essington of the University of Washington highlighted research on species and food web responses to low dissolved oxygen in the Salish Sea. Building on the robust discussion, Dr. Tessa Francis shared a proposal to describe potential risk to Puget Sound species (mostly fish) of low oxygen levels in marine waters, using existing modeling output and literature sources.


Sediment exchange 10.17.22

On October 17, 2022 we hosted a smaller, technical discussion about nutrient-related sediment exchange fluxes with the water column. Dr. David Shull shared insights from both historical and more recent monitoring. Then the discussion turned to how sediment exchange is represented in models, specifically LiveOcean and the Salish Sea Model, with experts like Dr. Parker MacCready. The group of experts reflected on some proposed modeling analysis, preliminary results, and how to refine our understanding of when and where sediment has an important impact on nitrogen cycling and low dissolved oxygen impacts.


Phytoplankton & Primary Production 12.06.22

On December 6, 2022 the University of Washington Puget Sound Institute hosted a workshop on Phytoplankton & Primary Production. This was a smaller, technical discussion about opportunities for coupled monitoring and modeling to address gaps in the science of primary production. This included some of the questions regarding inter-annual changes in seasonality and community structure in phytoplankton productivity, including the role of salinity gradient changes with climate change drivers. Dr. Sophia Johannesen with Fisheries and Oceans Canada, Dr. Maycira Costa with the University of Victoria, and Dr. Brian Hunt with the University of British Columbia shared insights from their research.


Watershed Modeling 12.12.22

The PSEMP Modeling Work Group and Puget Sound Institute co-hosted a Watershed Modeling workshop on December 12, 2022. The workshop included an overview of some watershed models and regional decision support tools, including the Hood Canal Landscape Assessment and Prioritization Tool, VELMA, SPARROW, Stormwater Heatmap, Water Quality Benefits Evaluation, and BasinScout. The discussion then turned to additional model linkages that support considering future scenarios like climate change with tools like the Land Cover Change Model, Envision, and Future Scenarios. Experts then reflected on knowledge gaps and shared inputs that could potentially benefit from collaborative improvements in the region.

The workshop just scratched the surface, so please share other regional models, tools, and future inputs through the Modeling Compendium Contribution Form.


Model evaluation group

Complex environmental challenges benefit from insights and ongoing advice from scientists in other regions. Which is why we are convening global experts in the Model Evaluation Group to complement regional efforts and advise Puget Sound Institute on how to improve the application of the model, related monitoring, and water quality management more broadly. The Model Evaluation Group will independently evaluate the application of the Salish Sea Model to support Puget Sound Recovery goals on water quality, including the model’s ability to support the determination of impacts and evaluate potential solutions. The Model Evaluation Group will summarize their recommendations in a technical memo and presentation.

Note: For more than 10 years the Salish Sea Model has evolved, with modules and refinement improving functionality and accuracy published in peer review literature4 so the Model Evaluation Group is not intended to conduct a full audit of the Salish Sea Model. It is also not intended to assess the regulatory standards.  

We are particularly excited to collaborate with scientists who have not only led cutting-edge research on dissolved oxygen, nutrient management, and modeling involving wastewater treatment plants but who have also implemented water quality strategies globally. These range from the Canadian fjords, to the Chesapeake Bay, to the Baltic Sea. Check out their experience for yourself. 

Meet the Model Evaluation Group

Bill Dennison

Professor of Marine Science and Vice President for Science Application at the University of Maryland Center for Environmental Science

Chairs the Science and Technical Assessment & Report team of the Chesapeake Bay Program, pioneering the use of environmental report cards in studies globally.

Bill Dennison leads the Integration and Application Network (IAN), a collection of scientists interested in solving, not just studying environmental problems. He was involved for ten years with the Healthy Waterways program in Queensland, Australia where an annual environmental report card has been produced since 2000. He joined the University of Maryland Center for Environmental Sciences in 2002 and is the inaugural chair of the Science and Technical Assessment & Reporting team of the Chesapeake Bay Program. Bill and his team of Science Integrators and Science Communicators have produced the Chesapeake Bay report card since 2006 and are involved in a suite of other regional environmental report cards with citizen science teams and various organizations.

Selected Publication: Environmental problem solving in coastal ecosystems: A paradigm shift to sustainability. 

Jacob Carstensen

Professor at Aarhus University, Denmark

Leads the Baltic Nest Institute that provides scientific input to countries engaged in the Baltic Sea Action Plan. Jacob’s research focuses on quantifying hypoxia and broader water quality issues and their drivers.

Jacob Carstensen is the Danish manager for the Baltic Nest Institute, a collaboration between Aarhus University, Stockholm University, and Finnish Environment Institute providing scientific input to HELCOM and national agencies as support for environmental policies in the Baltic Sea. His research has focused on assessing human impacts on marine ecosystems and identifying management responses to maintain good ecosystem functioning. Much of his research has been applied to the European Water Framework Directive, Marine Strategy Framework Directive, and HELCOM Baltic Sea Action Plan as well as national regulations. Jacob has published more than 160 papers in peer-reviewed journals, which have been cited ~14,000 times.

Selected Publication: Connecting the Dots: Responses of Coastal Ecosystems to Changing Nutrient Concentrations

Jeremy Testa

Associate Professor at University of Maryland Center for Environmental Science Chesapeake Biological Laboratory

Addresses critical challenges in biogeochemistry and dissolved oxygen modeling relevant to management, including predictive accuracy and uncertainty.

Jeremey Testa’s research focuses on coastal marine ecology, with an emphasis on the processes of eutrophication, nutrient cycling, dissolved oxygen dynamics, and ocean acidification. His group is especially interested in the interactions between biological, chemical, and physical processes in coastal ecosystems. They use a combination of experimental efforts, historical data analysis, and coupled biogeochemical-hydrodynamic modeling studies to examine these aspects of estuarine and coastal aquatic science.

Selected Publication: Inferring controls on dissolved oxygen criterion attainment in the Chesapeake Bay

Kevin Farley

Professor and the Blasland, Bouck and Lee Faculty Chair at Manhattan College

Advises the NY-NJ Harbor Estuary Program and has served on several national and international scientific review panels related to water quality and modeling, including for the Environmental Protection Agency (EPA), National Research Council, and United Nations Environment Programme (UNEP).

Kevin Farley researches and has served as a technical advisor on issues related to water quality, water quality modeling, sediment contamination, bioaccumulation of toxic contaminants, and metals. This has included serving on scientific review panels for the EPA Chesapeake Bay Program, the National Research Council Committee on Remediation of PCB-Contaminated Sediments, the EPA Science Advisory Board panel reviewing the agency’s risk assessment framework for metals, and the UNEP International Panel for Sustainable Resource Management Metals Workgroup. Kevin is currently serving as a member of the Science and Technical Advisory Committee for the NY-NJ Harbor Estuary Program and as a member of the Ecotoxicity Technical Advisory Panel for the international nonferrous metal industries.

Selected Publication: A Decision Support Framework to Facilitate Nitrogen Load Reductions in the Long Island Sound (LIS) Watershed

Peter Vanrolleghem

Professor at Université Laval, Canada

Chairs the Water Environment Federation (WEF) Modeling Expert Group of the Americas, and holds the Canada Research Chair in Water Quality Modelling.

Peter Vanrolleghem has published over 375 peer-reviewed papers, with a focus on modeling and control of activated sludge wastewater treatment processes, with special emphasis on model calibration and experimental design. Peter launched the BIOMATH research team that focuses on modeling methodologies for bioprocesses, mainly in environmental systems. Since 2006 he has been the Canada Research Chair on Water Quality Modeling, allowing him to start up the model EAU research team at Université Laval in Quebec City. Peter is also active on IWA’s Board of Directors, with the Réseau Environnement, and the Canadian Association on Water Quality, in addition to chairing the Modeling Expert Group of the Americas for WEF.

Selected Publication: Uncertainty in the environmental modelling process–a framework and guidance 


In 2020, Puget Sound Institute helped launch the Salish Sea Modeling Center. The Salish Sea Modeling Center’s mission is to: “provide access and use of Salish Sea basin-wide models of hydrology, hydrodynamics, circulation, transport, water quality, biogeochemistry, and ecosystem (food web) to our community for a wide variety of marine environmental applications.”2

Rachael Mueller is developing Puget Sound Institute’s nutrient-related modeling and model analyses. This includes collaborating with the Puget Sound Clean Water Alliance and King County on applied runs that will help inform municipalities’ optimization and capital investments. We are also coordinating with other researchers that use LiveOcean, SalishSeaCast, and the Salish Sea Model to refine our collective understanding of the temporal and spatial variability of nutrients and water quality impacts. Please email Rachael ( and Stefano ( if you have questions or are interested in additional analysis.

Our modeling is intended to build on and complement the Department of Ecology’s 2021 Optimization Scenario results and the next phase of modeling.

Related articles