WHATIF is software that integrates a number of calculators, tools, and models for assessing the health of watersheds and streams with an emphasis on fish communities in the Mid-Atlantic Highland region. The tool set consists of hydrologic and stream geometry calculators, a fish assemblage predictor, a fish habitat suitability calculator, macro-invertebrate biodiversity calculators, and a process-based model to predict biomass dynamics of stream biota (the BASS model). The tools can be used to assess conditions and associated stressors in aquatic ecosystems, to examine causes of impairment, and to forecast ecological outcomes of habitat alterations and fisheries management actions. WHATIF also supports screening analysis, such as prioritization of areas for restoration and comparison of alternative watershed and habitat management scenarios. The toolkit was developed for the Mid-Atlantic Highlands region of the United States in order to support Canaan Valley Institute.