Fish community structure, morphological characteristics, functional composition, and life history attributes in relation to three aquatic habitats, backwater shoreline (BWS), main channel borders (MCB), and side channel borders (SCB) in Pool 4 of the Upper Mississippi River System (UMRS) were assessed. Fish communities were sampled annually using standardized electrofishing techniques from 1994 to 2004. We found significant differences in community composition and abundance, and the clearest pattern was that diversity and fish community structure in BWS were different from those in both MCB and SCB. We also found morphological characteristics, functional composition, and life-history differences among the habitats, with fish communities from BWS having a number of different characteristics from both MCB and SCB. Temporal changes in fish abundance, community structure, morphological, functional and life-history attributes from each habitat may reflect both human impact and environmental factors on the Upper Mississippi River System.