The influence of specific types of habitat structure on fish assemblage structure, diversity and abundance in large rivers is largely unknown. This study determined whether fish assemblages differed among various artificial and natural habitats within the main channel border (shallow, nearshore areas) of the upper Mississippi River, and assessed whether different types of artificial structure influenced fish assemblage structure over long (>0.2 km) sections of shoreline habitat. Daytime electrofishing during August and October 1994 captured 31 different fish taxa from main channel border habitats in Pool 6 of the upper Mississippi River. Nine species of fish preferred specific types of nearshore habitat. Fish abundance and diversity measures differed little among habitat types, but significantly larger fish were present at locations with structure (wing dikes, woody snags) than at sites without (bare shore). Cluster analysis indicated that different fish assemblages occupied different habitat types. Riprapped shorelines had fish assemblages different from those in river sections containing only instream artificial rocky structures. Aggregations of various habitat types, especially artificial rocky structures, are important in determining fish assemblage structure within large river sections.