Variation in community composition (presence/absence data) and structure (relative abundance) of Upper Mississippi River fishes was assessed using data from the Long Term Resource Monitoring Program collected from 1994 to 2002. Community composition of fishes varied more in space than through time. We found substantial variation in community composition across two spatial scales: large-scale differences between upper and lower river reaches and small-scale differences among individual regional trend areas (RTA). Community structure (relative abundance data) of fishes also varied more through space than through time. We found substantial variation in fish community structure at three spatial scales: (1) large-scale differences between upper and lower river reaches, (2) differences among individual RTA, and (3) differences among habitat strata, with backwaters having a distinct community structure relative to the main channel and side channels. When averaged across all RTA, fish community structure in 1994 and 1995 was distinct from all other years, possibly as a result of the 1993 Flood. Fish community structure observations for each RTA and year correlated with the environmental variables measured at each sample site. A canonical approach revealed that the combination of Secchi depth, water temperature, current velocity, and vegetation abundance had the greatest correlation with community structure.