Effective fishery management necessitates understanding of resource partitioning by fishes that inhabit complex systems composed of biotic and abiotic features. Evaluations of non-native species introductions have continually demonstrated adverse effects associated with abundance and distribution of native fishes. Therefore, understanding resource selection and interactions between native and non-native species is important for recovery efforts. Habitat use by two native fish species (largescale sucker Catostomus macrocheilus [Girard] and mountain whitefish Prosopium williamsoni [Girard]) and one non-native fish species (pumpkinseed Lepomis gibbosus [Linnaeus]) of the Kootenai River, Idaho, were evaluated in a laboratory stream system. Trials were conducted in allopatry and in sympatry with and without the presence of wood to describe habitat selection in the context of on-going habitat rehabilitation efforts. Interactions were evident between native largescale sucker and non-native pumpkinseed concerning use of a woody structure and current velocity. Mountain whitefish used low-velocity habitats and selected locations that were further from wood when in sympatry with pumpkinseed. Our research suggests that habitat use of native, large-river fishes may be influenced by the presence of a non-native species, and that considering such interactions is critical when designing and implementing habitat rehabilitation efforts in river ecosystems.