Effective assessments of aquatic ecosystem recovery require ecologically sound endpoints against which progress can be measured. Site-by-site assessments of end points and potential recovery trajectories are impractical for water resource agencies. Because of the natural variation among ecosystems, applying a single set of criteria nationwide is not appropriate either. The article demonstrates the use of a regional framework for stratifying natural variation and for determining realistic biological criteria. A map of ecoregions, drawn from landscape characteristics, formed the framework for three statewide case studies and three separate studies at the river basin scale. Statewide studies of Arkansas, Ohio, and Oregon, USA, streams demonstrated patterns in fish assemblages corresponding to ecoregions. The river basin study in Oregon revealed a distinct change at the ecoregion boundary; those in Ohio and Montana demonstrated the value of regional reference sites for assessing recovery. Ecoregions can be used to facilitate the application of ecological theory and to set recovery criteria for various regions of states or of the country. Such a framework provides an important alternative between site-specific and national approaches for assessing recovery rates and conditions. (Copyright (c) 1990 Springer-Verlag New York Inc.)