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A habitat-change model was used to compare past, present, and future land cover and management practices to assess potential impacts of alternative agricultural practices on wildlife in two agricultural watersheds, Walnut Creek and Buck Creek, in central Iowa, USA. This approach required a habitat map for each scenario based on soil type and land cover, a list of resident species, and an estimate of the suitability of each of 26 habitat classes for every species. Impact on wildlife was calculated from median percent change in habitat area relative to the present. Habitat classes with the highest species richness for native vertebrates were ungrazed riparian forest, upland forest and wet prairie. Differences in habitat composition and configuration were evident among maps of the watersheds for the past, present, and three alternative future scenarios (Production, Water Quality, and Biodiversity). The Production scenario ranked lowest in providing habitat for all native taxa. For most taxa, changes in wildlife habitat due to land use changes in the Biodiversity, Water Quality, and Past scenarios were similar, resulting in greater habitat than either the present landscape or the Production scenario. For native birds, amphibians, mammals, and rare species in both watersheds, the Biodiversity scenario ranked highest in providing habitat, and the Water Quality scenario was similar to or slightly below the Biodiversity scenario. The Water Quality scenario was similar to or slightly better than the Biodiversity scenario for reptiles and butterflies in both watersheds, and both ranked higher than the Production scenario for these taxa.