We sampled fishes at 17 inner bend sites on the Wabash River in 2008 to compare with collections from 1977 to 1997. We used the same seine collection methods as previous years and collected a total of 37 species. Mean site Shannon‐Wiener diversity, species richness, evenness and abundance for all years were similar. We used multivariate analyses to test for patterns in fish assemblage structure among all sites and all years. The multivariate analyses resulted in distinct assemblages for each collection‐year, suggesting shifts in assemblage composition among years. We used separate multivariate analyses to examine fish assemblage variation within individual years. Variation that corresponded to an upstream–downstream pattern was present in 1977 and 2008, but not in 1997. A hydrologic analysis based on daily discharge revealed that eight large flood events occurred from 1928 to 2007, with four of these events during the recent 20 years. We quantified substrate variation at the 17 sites in 2008 and identified a longitudinal gradient in dominant substrate categories with gravel upstream and sand downstream that was correlated with the first axis of the 2008 fish assemblage ordination. We suggest that observed changes in fish assemblages in decadal periods were from hydrologic impacts of large floods on local habitats. Copyright © 2010 John Wiley & Sons, Ltd.