As part of a regional study by the Atlantic Slope Consortium (ASC) to develop ecological and socioeconomic indicators of aquatic ecosystem condition, we developed and tested a protocol for rapidly assessing condition of the stream, wetland, and riparian components of freshwater aquatic ecosystems. Aspects of hydrology, vegetation, in-stream and wetland characteristics, and on-site stressors were measured in the field. The resulting metrics were used to develop an index of overall condition, termed the Stream-Wetland-Riparian (SWR) Index. Values of this Index were compared to existing biotic indices and chemical measures, and to a Landscape Index created using satellite-based land cover data and a geographic information system (GIS). Comparisons were made at several levels of spatial aggregation and resolution, from site to small watershed. The SWR Index and associated Landscape Indices were shown to correlate highly with biological indicators of stream condition at the site level and for small contributing areas. The landscape patterns prevalent throughout the entire watershed do not necessarily match the patterns found adjacent to the stream network. We suggest a top-down approach that managers can use to sequentially apply these methods, to first prioritize watersheds based on a relative condition measure provided by the Landscape Index, and then assess condition and diagnose stressors of aquatic resources at the subwatershed and site level.