Knowledge of how patterns in fish assemblages are spatially structured is important for guiding management and conservation actions. However, most studies have taken place in the eastern and midwestern U.S., resulting in a poor understanding of factors influencing western stream fishes. The objectives of this study were to evaluate habitat and species associations of fishes in Deep Creek, a small tributary of the Kootenai River in Idaho. Fishes and habitat were sampled from 58 reaches in Deep Creek. In total, 7,129 individual fishes representing 18 species were sampled. Patterns in species richness were largely a function of channel gradient and associated habitat characteristics. Species richness decreased with increased channel gradient. Species-specific habitat relationships for native and nonnative fishes in Deep Creek provided specific insights into the ecology of each species. Predicted probability of occurrence and relative abundance varied by species and were related to a broad suite of environmental characteristics. This study provides insight on patterns of fish assemblage structure, as well as important information on the ecology of native and nonnative fishes in a western stream system.