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The difference between management objectives focused on sustainability of fish populations and the indigenous aquatic community, and a management objective focused on minimizing entrainment and impingement losses accounts for much of the ongoing controversy surrounding §316(b). We describe the EPA’s ecological risk assessment framework and recommend that this framework be used to more effectively address differences in management objectives and structure §316(b) determinations. We provide a blueprint for the problem formulation phase of EPA-type ecological risk assessments for cooling-water intake structures (CWIS) at existing power plant facilities. Our management objectives, assessment endpoints, conceptual model, and generic analysis plan apply to all existing facilities. However, adapting the problem formulation process for a specific facility requires consideration of the permitting agency’s guidelines and level of regulatory concern, as well as site-specific ecological and technical differences. The facility-specific problem formulation phase is designed around the hierarchy of biolo gical levels of organization in the generic conceptual model and the sequence of cause-effect events and risk hypotheses represented by this model. Problem formulation is designed to be flexible in that it can be tailored for facilities where §316(b) regulatory concern is low or high. For some facilities, we anticipate that the assessment can be completed based on consideration of susceptibility alone. At the other extreme, a high level of regulatory concern combined with the availability of extensive information and consideration of costly CWIS mitigation options may result in the ecological risk assessment relying on analyses at all levels. Decisions on whether to extend the ecological risk assessment to additional levels should be based on whether regulatory or generator concerns merit additional analyses and whether available information is adequate to support such analyses. In making these decisions, the functional dependence between levels of analysis must be considered in making the transition to the analysis phase and risk estimation component of the ecological risk assessment. Regardless of how the generic analysis plan is modified to develop a facility-specific analysis plan, the resulting plan should be viewed as a tool for comparing representative species and alternative CWIS options by focusing on relative changes (i.e., proportional or percent changes) in various measures. The analysis plan is specifically designed to encourage consideration of multiple lines of evidence and to characterize uncertainties in each line of evidence. Multiple lines of evidence from different levels of analysis, obtained using both prospective and retrospective techniques, provide a broader perspective on the magnitude of potential effects and associated uncertainties and risks. The implications of the EPA’s recent (April 2002) proposed regulations for existing facilities on the applicability of this blueprint are briefly considered.