The Waquoit Bay Watershed ecological risk assessment was performed by an interdisciplinary and interagency workgroup. This paper focuses on the steps taken to formulate the analysis plan for this watershed assessment. The workgroup initially conducted a series of meetings with the general public and local and state managers to determine environmental management objectives for the watershed. The workgroup then decided that more information was needed on the impacts of six stressors: nutrient enrichment, physical alteration of habitat, altered freshwater flow, toxic chemicals, pathogens, and fisheries harvesting. Assessment endpoints were selected to establish the link between environmental management objectives, impacts of stressors, and scientifically measurable endpoints. The following assessment end-points were selected: estuarine eelgrass cover, scallop abundance, finfish diversity and abundance, wetland bird distribution and abundance, piping plover distribution and abundance, tissue contaminant levels, and brook trout distribution and abundance in streams. A conceptual model was developed to show the pathways between human activities, stressors, and ecological effects. The workgroup analyzed comparative risks, by first ranking stressors in terms of their potential risk to biotic resources in the watershed. Then stressors were evaluated by considering the components of stressors (e.g., the stressor chemical pollution included both heavy metals and chlorinated solvents components) in terms of intensity and extensiveness. The workgroup identified nutrient enrichment as the major stressor. Nutrient enrichment comprised both phosphorus enrichment in freshwater ponds and nitrogen enrichment within estuaries. Because phosphorus impacts were being analyzed and mitigated by the Air Force Center for Environmental Excellence, this assessment focused on nitrogen. The process followed to identify the predominant stressor and focus the analyses on nitrogen impacts on eelgrass and scallops will serve as an example of how to increase the use of the findings of a watershed assessment in decision making.