Thesis (M.S., Natural Resources) | A comparison of sampling techniques and investigation of fish assemblage structure is greatly needed to improve management of western river systems. The objective of this thesis was to compare the efficacy of several gears (hoop nets, boat-mounted electrofishing, benthic trawls) for sampling fish assemblages of western rivers (Green River, Wyoming; Kootenai River, Idaho) and to investigate patterns of fish assemblage shifts in relation to habitat in the Kootenai River. In general, species-specific detectability varied by system and habitat, but was most influenced by gear. Electrofishing and hoop nets had the highest detection probabilities for most species, whereas detectability of most fishes was low with trawls. Transitions in fish assemblage and habitat structure were apparent among river sections in the Kootenai River. This thesis provides information that will improve sampling efficiency and our understanding of factors that structure fish assemblages and populations in coldwater rivers.