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Summary A set of methods are developed and demonstrated for setting clear and measurable fish community targets for environmental restoration in contemporary waterways. Two case studies illustrate the application and value of these methods: a small northeast United States river and the Hudson River estuary in New York City. A target fish community can be used to diagnose impediments to a desired fish fauna, define needed restoration activities, and identify precisely the fish community for restoration. A target fish community defines species composition and community proportions by species. In the small river case, observed fish community had underrepresented species that were mostly fluvial fishes and overly abundant species that were mostly habitat generalists or lentic oriented species. Results indicated flowing water habitat improvement was the highest priority. The estuary case defined species composition and community proportions for shorelines in New York City. While this estuarine ecosystem had a high diversity of fishes and few missing species, the shoreline community was determined to be highly biased toward fishes using open pelagic waters. Departures from target conditions were used to define clear and practical restoration needs in this intensely urbanized waterway: shallow shoreline waters with cover. Integrating restoration policy, objective zoogeography analyses, and theory-based parameters of community structure yields restoration specifications that are future oriented, meaningful to the public, and scientifically justified. [ABSTRACT FROM AUTHOR]