Multiscale environmental processes determine in-stream habitat conditions which drive species distributions. Habitat constitutes the physical template upon which ecological processes occur and species conduct life stage activities. Habitat heterogeneity promotes biodiversity of aquatic systems. Stream classification informs freshwater conservation by providing a useful framework to account for habitat heterogeneity, often based on landscape regions of similar environmental processes. A greater understanding of landscape-based classification frameworks as means to classify stream systems may improve understanding of drivers of biodiversity. Using Nebraska as a case study, on a statewide scale, objectives were 1) to characterize habitat availability for several at-risk fish species, and 2) to assess the categorization of stream habitat heterogeneity within multiple classification systems. Species distribution models provide a tool to characterize spatial habitat patterns and quantify species-habitat relations. Species distribution models were constructed from environmental data and historical presence data for 3 at-risk cyprinid species including Flathead Chub, Plains Minnow, and Northern Redbelly Dace. Our results support current knowledge of impactful habitat features based on species traits and environmental processes shaping site-scale habitat conditions. For all 3 species, hydrological factors such as flow velocity and discharge were among the most influential habitat conditions of examined variables. Further, variables representing stream size and position in the drainage network consistently carried high influence. We used site-level stream data collected by the Nebraska Department of Environment and Energy (NDEE) from 1995-2021 to assess stream habitat heterogeneity among Biologically Unique Landscapes (BUL) at a statewide spatial scale. Multivariate cluster analysis and statistical similarity tests were used to determine if aquatic habitat within the BULs is unique and by which features they vary. No significant differences were found between aquatic environmental conditions within and outside BULs. Evidence for unique aquatic habitat conditions among BULs was limited, shown in minimal pairwise differences among BULs in statistical similarity tests. Furthermore, the classificatory power of the BULs underperformed all other classifiers and, as such, BULs may not improve statewide stream classification.