The report presents the results of a project to develop subbasin profiles of resources, indicators of impairment, and stressors (pollutant sources) and to identify areas critical to protecting and restoring the system. The data summarized in the report support the continuing focus of regional restoration efforts for the Neuse River and Pamlico River estuaries. The watersheds of these estuaries have the most intense level of activity, and these waterbodies appear to be experiencing the most stress. Other waterbodies harbor important resources and exhibit some symptoms of degradation; however, it is suggested that the most pressing conflicts between human activities and ecological resources are occurring in the Neuse and Pamlico basins and projections of future population increases suggest this conflict will continue.