Watersheds are frequently used to study and manage environmental resources because hydrologic boundaries define the flow of contaminants and other stressors. It is a challenge to incorporate scientific information in watershed management and planning. Ecological assessments of watersheds are complex because watersheds typically overlap multiple jurisdictional boundaries, are subjected to multiple environmental stressors, and have multiple stakeholders with diverse environmental and socioeconomic interests. Ecological Risk Assessment (ERA) is an approach that has successfully been used to increase the use of ecological science in decision making, by evaluating the likelihood that adverse ecological effects may result from exposure to one or more stressors, yet its application to watershed assessment is limited. The purpose of this report is to provide suggestions and examples for making scientific information more relevant to the needs of watershed managers by using ERA principles to help structure ecological assessments of watersheds. This report supplements the 'Guidelines for Ecological Risk Assessment', PB98-117849, by addressing issues commonly encountered when conducting watershed ecological assessments. Suggestions and examples to follow are provided based upon lessons learned from prior watershed ERA's. This report is of potential use to ecologists, hydrologists, watershed managers, risk assessors, landscape ecologists, and other scientists and managers seeking to increase the use of environmental assessment data in decision making. Each activity and phase of the watershed ERA process is explained sequentially in this report. Guidance on how to involve stakeholders to generate environmental management goals and objectives is provided. The processes for selecting assessment endpoints, developing conceptual models, and selecting the exposure and effects pathways to be analyzed are described. Suggestions for predicting how multiple sources and stressors affect assessment endpoints are also provided; these include using multivariate analyses to compare land use with biotic measurements. In addition, the report suggests how to estimate, describe, and communicate risk and how to evaluate management alternatives.