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 electrofi shing techniques from 1994 to 2004. We found signifi cant diff erences in community composition and abundance, and the clearest pattern was that diversity and fi sh community structure in BWS were diff erent from those in both MCB and SCB. We also found morphological characteristics, functional composition, and life-history diff erences among the habitats, with fi sh communities from BWS having a number of diff erent characteristics from both MCB and SCB. Temporal changes in fi sh abundance, community structure, morphological, functional and life-history attributes from each habitat may refl ect both human impact and environmental factors on the Upper Mississippi River System. © Koninklijke Brill NV, Leiden, 2009.