Nonwadeable or large rivers are dynamic aquatic ecosystems capable supporting high fish biodiversity. Due to human activities on the landscape and in waterways, large rivers and their associated fish assemblages have become increasingly imperiled. It is essential to understand fish response to human activities in order to provide effective management and conservation measures. In response to these concerns, our objectives were to 1) evaluate the historic changes in fish assemblages that occurred in Iowa's interior nonwadeable rivers via representative changes occurring in five focal river systems and 2) determine the relationship between fish assemblage structure and environmental characteristics measured at multiple spatial-scales. In the first objective, historic change in fish assemblage was evaluated in the mainstems of the Des Moines, Iowa, Cedar, Wapsipinicon, and Maquoketa rivers, in Iowa. Fish occurrence data were compared in each river between historic and recent time periods to characterize temporal changes among 126 species distributions and assess spatiotemporal patterns in faunal similarity. A resampling procedure was used to estimate species occurrences in rivers during each assessment period and changes in species occurrence were summarized. Shifts in species composition were analyzed at the river and river section scale using cluster analysis, species turnover, and analysis of multivariate beta dispersion. The majority of species exhibited either increases or declines in distribution in all rivers with the exception of several "unknown" or inconclusive trends exhibited by species in the Maquoketa River. Cluster analysis identified temporal patterns of similarity among fish assemblages in the Des Moines, Cedar, and Iowa rivers within the historical (AU = 0.92) and recent (AU = 0.95) assessment period indicating a significant change in species composition. Prominent declines of backwater species with phytophilic spawning strategies contributed to assemblage changes occurring across river systems. In the second objective, we evaluated the relationship between fish assemblage structure and landscape-scale, dam-related, and reach-scale environmental characteristics. In the summers of 2011 and 2012, comprehensive fish and environmental data were collected from 33 reaches in the Iowa and Cedar rivers of eastern-central Iowa. Canonical correspondence analysis (CCA) was used to evaluate environmental relationships with species relative abundance, trait abundance (e.g., catch rate of tolerant species), and trait composition (e.g., percentage of tolerant species). Variance partitioning from partial CCAs identified that reach-scale environmental characteristics contributed the majority of variance in fish assemblages described in the CCA models. Relative to landscape characteristics, dams explained a considerable amount of variation in the CCAs. Among the reach-scale variables, mean annual discharge was consistently selected in CCA models and accounted for the majority of explained variance among reach-scale variables. Dominant discharge patterns suggested that fish assemblages were primarily structured longitudinally, corresponding with changes in discharge.