Lake Erie and its tributaries have experienced extensive changes in environmental conditions and community structure during recent decades. To assess the relative importance of environmental conditions in determining fish community composition, fish communities and their associated environmental conditions were sampled from the lower reaches and mouths of the tributaries flowing into the northeastern basin of Lake Erie. These data were used to assess relationships between habitat and fish community composition on spatial and temporal scales using correspondence analysis and canonical correspondence analysis. Multivariate analyses revealed that the fish assemblage was size structured and related to water chemistry but also showed influences due to temperature, sampling date and aquatic macrophytes. The community composition showed the effects of biotic interactions, predominantly negative predator-prey associations, but there were also assemblage differences specific to particular tributaries and sampling methodologies.