Thesis (M.S., Natural Resources) -- University of Idaho, 2016 | Fish and microhabitat data were collected at 542 locations in the Kootenai River, Idaho, during 2014 and 2015 to evaluate the effects of habitat rehabilitation on the fish assemblage. Samples were collected from locally-treated and locally-untreated areas of the river to investigate habitat conditions related to the occurrence and relative abundance of fishes. Fishes sampled from backwaters composed 71% of the overall catch and 84% of the catch from locally-untreated areas of the river. Assemblage-level ordinations and population-level regression models suggested that water depth and current velocity were the most important microhabitat variables influencing fish assemblage structure. Specifically, shallow habitats with low current velocities were important for native fishes and likely serve as rearing areas. These microhabitat conditions typically characterize backwater and channel-margin habitats that are vulnerable to anthropogenic perturbation. Conserving these habitats in large, regulated rivers would enable natural channel forming processes for the benefit of native fishes.