Fish community data were collected to investigate the role of wetlands in supporting fish communities of protected embayments in Lake Ontario. Wetland and deeper, more open, littoral sites were sampled in five protected embayments using gill nets, fyke nets, minnow traps, and electrofishing gear during the summers of 2001 and 2002. Pooled gear data were used to analyze community composition, size frequency, and species richness. We found that even within protected embayments where community composition of both habitats is similar, wetlands support a community of fish different in species dominance and size structure than littoral embayment habitats. The abundance of young-of-year fish suggests that wetlands support fish populations by providing important nursery habitat. The similarity in fish community composition between wetland and littoral habitats indicates that wetlands remain important in supporting a subset of the embayment fish community. These results demonstrate that both wetlands and littoral areas in embayments are valuable and intensively utilized fish habitats that should receive special consideration in ecosystem management plans for the Great Lakes.