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Goal - Clean Water

Aquatic Stressors Research

Agency problem

The Clean Water Act provides a legislative mandate to EPA to maintain and restore the biological and chemical integrity of the Nation's waters. Preservation of these aquatic resources requires the development of scientifically based ecological criteria protective of designated uses. A failure to meet designated use caused by one or more stressors results in a Section 303d listing under the Clean Water Act, requiring that states establish total maximum daily loadings (TMDLs) to ameliorate the problem. While there have been major advances in methods to evaluate the effects of point-source discharges to aquatic systems, significant uncertainties remain with respect to defining system responses to stressors such as excess nutrients, sediments and habitat alteration. An improvement of the ability to model stressor-response relationships is critical to the establishment of ecological criteria protective of aquatic resources.

Many anthropogenic activities (e.g. land-use changes, hydrologic modification, climate change, altered biological diversity, introduction of nonnative species) exert their influence on biota via effects on habitat. As a consequence, habitat alteration is arguably the most important cause of declines in ecological resources in North America (EPA 1990). Habitat alteration is a common cause for the failure of aquatic systems to meet designated uses as required by the Clean Water Act (CWA). Addressing failures to attain designated uses increasingly requires an integrated approach perhaps best provided by habitat-based criteria. As required by the Endangered Species Act, EPA is increasingly being asked to participate in interagency species protection and restoration efforts where habitat issues play a key role. Synthetic rather than piece-meal approaches to environmental protection require that the importance of habitat on various spatial scales be quantified. Because one of EPA’s core ecological regulatory authorities is the CWA, the species endpoints for which habitat alteration is of greatest concern are aquatic species.

WED research seeks to improve stressor-response models. The principal clients for this research include the EPA Office of Water, the EPA Regional Offices, and state, tribal, and local governments.

Science Problems

Aquatic stressor research at WED is concentrated in two ecosystem types, estuaries and freshwater streams.

Estuaries: The Pacific Coastal Ecology Branch (PCEB) focuses on estuarine ecology, with particular emphasis on nutrient processes. Excessive nutrient loading has been identified as one of the principal anthropogenic stressors on coastal ecosystems. Excessive nutrients may derive from point sources, but are increasingly a consequence of human activities in the surrounding watershed. The elevated nutrient levels may alter the estuarine food web in many ways, causing the estuarine ecosystem to diverge from its designated use. Submerged aquatic vegetation (SAV) is one important estuarine habitat, both as a primary producer and a source of food and shelter for other organisms. SAV is known to respond negatively to augmented nutrient levels, and loss or alteration of SAV habitat may have important effects on other estuarine species. SAV is also a potentially important indicator of integrated estuarine water quality and condition. Other habitats defined by ecological engineering species such as burrowing shrimp have similar importance to the estuarine system both in terms of nutrient dynamics and direct influence on other species.

Important scientific questions being addressed in order to improve protective criteria are:

How do excessive nutrients affect the food web structure of Pacific Northwest estuaries? How can such impacts best be modeled?

How do important estuarine habitats (SAV, burrowing shrimp) respond to stressors such as nutrients, sediments, and other forms of disturbance? How does habitat alteration affect species dependant on these habitats?


Project Leader for all Estuarine Ecology Research Efforts - James Power

Nutrients and Estuarine Food Web Modeling

Principal Investigators:

Addition of excess nutrients into estuarine ecosystems typically results in major alterations in the cycling of carbon and nutrients through the components of the food web. PCEB researchers are developing an estuarine food web model that will allow managers to identify critical food web flows where small changes in a component can cascade through the ecosystem and result in eutrophication, extinction of important habitats, or changes in ecosystem trophic structure. To fully encompass population, community, and ecosystem processes, the PCEB model uses natural abundance of carbon (13C) and nitrogen (15N) stable isotopes to examine the relationships between organisms, habitats, and the estuary ecosystem. The model also incorporates other available data concerning organism biomass production and transport within and external to the estuary. The result is a full description of carbon and nitrogen material flows in estuaries. Separate models of estuaries subjected to various types and levels of multiple stressors can be used to determine the mechanistic links between stressors and effects within estuaries.

Submerged Aquatic Vegetation Stress Response Modeling

Point of Contact: James Kaldy - Phone: 541-867-4026, Email - kaldy.jim@epa.gov

Principal Investigators:
  • Christian Andersen
  • Bruce Boese
  • Mark Johnson
  • David Young
  • The goal of this research is the development of a series of models to address the response of seagrass to nutrient and other anthropogenic and natural stressors. The principal model will predict changes in the biomass of the above- and below-ground components of seagrass standing stock. This seagrass model will be coupled to a sediment diagenesis model which will allow prediction of changes in seagrass biomass resulting from changes in deposition of organic matter to the sediments. A seagrass physiology model is being developed to assist in calibration of the principal seagrass model. A third model will assess variations in areal distribution of seagrasses in response to stressors. The research effort will couple field monitoring and direct experiments with model development to test the predicted responses of seagrass to stressors.

    Estimation of Changes in Habitat Value at Estuarine Scale

    Point of Contact: James H. Power - Phone: 541-867-4027, Email - power.jim@epa.gov

    Principal Investigators:

    The goal of this research is to develop methods to predict estuarine scale changes in relative habitat value resulting from anthropogenic habitat alteration. Pacific Northwest estuaries are frequently dominated by a few species that are characterized as "ecosystem engineers", meaning that their presence and activities strongly influence the physical, chemical, and biological attributes of the surrounding estuarine ecosystem. Two important types of ecosystem engineers are seagrasses and burrowing shrimp. Patches of seagrass stabilize the sediment, affect the surrounding water column chemistry, and most importantly provide food and shelter for a wide number of other estuarine organisms. Burrowing shrimp also affect water column chemistry, and are capable of extreme bioturbation of the sediment, resulting in the exclusion of seagrass and commercially important oysters.

    Indicators of Estuarine Condition

    Point of Contact: Bruce Boese - Phone: 541-867-5019, Email - boese.bruce@epa.gov

    Principal Investigators:

    PCEB is evaluating several indicators of relevance to western estuaries. One of these is seagrass distribution, which is being evaluated as an estuarine scale indicator integrating multiple aspects of estuarine water quality. Research seeks to define a theoretical baseline condition for Zostera marina for PNW estuaries by defining the lower depth limit as set by water column light availability, by establishing determinants of the upper intertidal boundary, and by determining spatial variation due to wind-generated wave stress, sediment type and quality, salinity tolerance, and extent of potential biological competitors.

    The alteration of coastal systems by non-indigenous species (NIS) is of steadily expanding concern. A variety of indicators of the impact of NIS are being evaluated, including percent abundance of NIS, percent frequency of NIS, percent of total species composed of NIS, number of NIS species, and density of NIS.


    Freshwater Streams: NHEERL has initiated a nationwide research program to quantitatively link alterations in key habitats to fish, shellfish, and wildlife endpoints because habitat alteration is such an important, pervasive stressor on valued aquatic resources. The research involves all four ecological divisions of NHEERL and spans the coastal resources of the East, West, Gulf states, and the Upper Midwest. The purpose of the research described in this plan is to provide the scientific basis to implement regulations and policies to protect fish, shellfish, and wildlife populations and the ecosystems upon which they depend. An important component of this research focusing on the wild Pacific Salmon and other native fish of the Pacific Northwest.


    To evaluate and to quantify the influence of human activities at the landscape and watershed scales on native fish habitat and wild Pacific Salmon and native fish populations.

    To evaluate how habitat spatial structure and connectivity of habitat in stream networks and estuaries influence wild Pacific salmon and native fish populations.




    Project Leader: Jim Wigington - Phone: 541-754-4341, Email - wigington.jim@epa.gov

    Principal Investigators:

    Research Support:

    In the Pacific Northwest (PNW), many populations of wild anadromous salmonids are in serious decline.  Landscape change, water pollution, introduced predators, fishing, hydropower development, hatcheries, disadvantageous ocean conditions, and other factors have led to the extinction or decline and listing of many stocks under the Endangered Species Act.  Because of the national policy significance of Pacific salmon population declines,  EPA’s National Health and Environmental Effects Research Laboratory (NHEERL) has assigned the Western Ecology Division the responsibility of conducting habitat-related research that will contribute to overall interagency efforts to restore viable populations of wild salmon and other native fishes in the Pacific Northwest. This research is part of a larger nationwide NHEERL research program that is designed to provide the scientific basis for assessing the role of essential habitat in maintaining healthy populations of fish, shellfish, and wildlife and the ecosystems on which they depend.  For the research project described herein, our overall goal is: 

    To quantify the influence of human and natural disturbances at landscape and watershed scales on salmon populations and native fish assemblages in Oregon coastal streams. 

    We have chosen to focus our research in Oregon coastal streams for a number of reasons.  First, salmon populations in the Oregon coastal drainages have experienced declines similar to those experienced throughout the Pacific Northwest. Coho salmon (Oncorhynchus kisutch) is the most notable salmonid species that has been listed as threatened by the National Marine Fisheries Service (NMFS).   Secondly, there appears to be good potential in coastal streams, such as those in Oregon, to restore viable salmon populations. Coastal streams are generally free flowing, with few dams and reservoirs. Also, there are great opportunities for collaborative research with agencies and organizations

    Salmon-Derived Nutrients Project

    Project Leader:  Jana Compton - Phone: 541-754-4620, Email: compton.jana@epa.gov

    Principal Investigators:

    The decline of Pacific salmon populations is a key issue in the Pacific Northwest, influenced by a complex set of human activities and large-scale climatic factors. The return of adult salmon may be an important pathway of nutrient supply to Pacific coastal watersheds. Since present-day salmon returns are approximately 5% of historical returns in coastal Oregon and Washington, the loss of salmon-derived nutrients could have important consequences for aquatic, riparian and terrestrial ecosystems. Recent work demonstrated that salmon-derived nutrients are incorporated into riparian and freshwater food webs, and for this reason, managers and public interest groups are beginning to advocate the restoration of this pathway via nutrient additions to affected ecosystems. However, the ecological and water quality consequences of such additions have not been widely examined. Because coastal watershed management can involve a range of land uses that influence many ecosystem services, it is important for managers and regulators to know the broad effects of nutrient additions.

    To determine the consequences of declining salmon-derived nutrient supply to Pacific coastal watersheds, we are assembling databases on land-cover, returning adult salmon, and watershed nutrient export for both present-day and historical conditions. Reconstruction of riparian forest history will be used as a tool to determine and isolate the long-term effects of climate and salmon-derived nutrients. We plan to examine ecological processes and water quality across natural gradients in salmon-derived nutrients.

    The goals of the Salmon-Derived Nutrient project are: 1) to determine the ecological consequences of the decline in salmon-derived nutrients for Pacific Coastal watersheds, 2) to identify the interactions between food resources and physical habitat, two important factors influencing aquatic ecosystems and salmon populations, and 3) to provide information for scientists, managers and regulators concerning the effects of nutrient additions on water quality and freshwater and riparian ecosystems.


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