Fish sampling was conducted over a two-year period (May to August, 2004 and 2005) in seven streams traversing the Little Missouri River National Grassland and Theodore Roosevelt National Park, western North Dakota. Fish communities of the two stream types in the region (rolling prairie and badlands) differed significantly despite their close geographic proximity, overlapping by only 18% in species composition and having only 8 of the 21 total fish species in common. As summer progressed, rolling prairie streams showed an increase in total fish density while total fish density in badland streams decreased. Badland and rolling prairie stream fish communities responded differently to the physical habitat variables of pool surface area, volume, mean depth, maximum depth, and width-to-depth ratio. Fish in badland streams appeared to be more susceptible to rapid physical habitat changes associated with late summer dewatering, while the more stable flows of rolling prairie streams prevented significant isolation of individuals in pools. Livestock grazing produced no significant detectable impacts to aquatic habitat availability. Streams within the region have always been subjected to contrasting natural periods of flood and drought, along with legacy effects of intensive domestic livestock grazing for more than a century. Conditions that impact fish assemblage structure, abundance, distribution, and survival are strongly influenced by changing physical habitat conditions such that the fish communities persist opportunistically within environmental instability. Naturally harsh, highly variable conditions and a lack of adequate experimental domestic livestock exclosures complicate proper evaluation of effects of land use practices. Establishment of some long-term, extensive exclosures over a period of years or decades would facilitate the evaluation of the roles of abiotic factors, biotic factors, and land use practices in shaping fish communities.