The Missouri River has been subjected to human alteration for over 150 years and the flow regime is one physical attribute that has drastically changed as a result of alteration. Likewise, using flow characteristics has been identified as a driving variable to describe fish community structure in lotic systems. Therefore, my goal was to assess fish community structure in the Missouri River system in relation to flow. I first used a time series approach to examine daily mean flow data from 10 gauging stations on the Missouri River, and tested for differences associated with human alteration. Daily mean flow over the entire year was significantly higher for the post-alteration period (1966--1996) compared to the pre-alteration period (1925--1948) reflecting long-term differences in precipitation. Daily mean flows over a spring fish spawning period (1 April--30 June) were significantly lower in reaches influenced by impoundments suggesting that human alterations have resulted in changes to the natural spring flow regime;I then used a multivariate approach to group post-alteration daily mean flow data from 15 gauge stations along the Missouri and lower Yellowstone Rivers. I identified six hydrologically distinct units composed of gauge stations exhibiting similar flow characteristics based largely on flow variability and predictability. I then explored fish community structure, functional composition, and life-history attributes in relation to these six flow regimes where altered areas are thought to be dominated by generalist type species. My results suggest this to be true as the units most influenced by the reservoirs (i.e., most altered) did have a higher percentage of generalist species;The final focus of this study was to evaluate growth rates over a latitudinal gradient for five fish species (channel catfish Ictalurus punctatus ; emerald shiners Notropis atherinoides; freshwater drums Aplodinotus grunniens; river carpsuckers Carpiodes carpio; saugers Stizostedion canadense). Species specific growth rates were different (P < 0.05) for each section of river analyzed. Most species displayed some regional trends in growth rate but river-wide patterns were largely inconclusive. However, emerald shiners did exhibit higher growth grates with an increase in latitude. Based on these results, improved flow management in the heavily altered areas of the Missouri River may facilitate rehabilitation of the native fish community.