Sampling was conducted over a two-year period to determine if fish body morphology (as indicated by the Fineness Ratio (FR), an index of fish streamlining) and habitat alterations can interact to influence fish assemblage structure in three human-altered segments of the Missouri River. It was hypothesized that segments with more variability in depths, velocities, and substrates would have a fish assemblage characterized by more diversity in streamlining. Conversely, it was hypothesized that fish assemblages in more altered river segments would exhibit less diversity in streamlining, i.e., less variability from optimal values because of more uniform habitat conditions. In faster more uniform habitats, fewer variations from optimal streamlining would be adaptive. The three flowing segments studied encompassed the mouth of the Yellowstone River (YSS; moderately altered), the area below Garrison Dam, North Dakota (GOS; below dam-highly altered) and the segment from St. Joseph to Kansas City, Missouri (SKS; channelized-highly altered). The three segments exhibited greatly different fish assemblages. Small native minnows (Cyprinidae), particularly flathead chub (Platygobio gracilis), and deep-bodied suckers, such as bigmouth buffalo (Ictiobus cyprinellus), were common in the YSS. The GOS was dominated by the dorsally compressed fathead minnow (Pimephales promelas). Emerald shiner (Notropis atherinoides) and gizzard shad (Dorosoma cepedianum) dominated the fish assemblage in the SKS. When FR and physical conditions were analyzed across all habitat types, the least altered, more natural YSS was characterized by higher diversity of FR and higher variability in velocity and depth than the most altered SKS. Results for the GOS were more difficult to interpret. The fish assemblage in the highly channelized SKS exhibited the weighted mean FR that was closest to the optimal 4.5 value (FR = 4.42) with the smallest deviation from optimal (0.08). The highest mean and highest maximum current velocity use in the three segments was found for species such as sicklefin chub (Macrhybopsis meeki), sturgeon chub (Macrhybopsis gelida), and blue sucker (Cycleptus elongatus), that were nearly optimally streamlined. Deep-bodied species with FRs typically below 3.5, such as Ictiobus spp., river carpsucker (Carpiodes carpio), and centrarchids, tended to exhibit the lowest mean and lowest maximum current velocity use in the three segments . Results of this study can be useful in helping to understand fish assemblage composition in relation to river alterations in various geographical areas. Because the fineness ratio is only a simple index of streamlining and does not account for other anatomical (e.g., fins) and behavioral aspects of fishes, more studies on different species are needed to develop a stronger understanding of how fish cope with the current. Because of the complexity of interacting natural and human-caused factors affecting these highly altered large river systems, fish streamlining is only one of several factors that may influence the observed fish community structure of a large river system. Streamlining deserves consideration, however, for inclusion in more complex models explaining and predicting fish community structure in large rivers.