In this study we evaluated changes in benthic invertebrate communities of South Bay, Lake Huron following the invasion of zebra mussels (Dreissena polymorpha) and considered the implications for diets and growth of whitefish (Coregonus clupeaformis), a commercially important fish in the Great Lakes. Of the ten benthic invertebrate groups identified prior to invasion (1980–81), only densities of Diporeia and Oligochaeta have changed since the appearance of the zebra mussel, and only Diporeia and Chironomidae changed in relative abundance. These changes are similar to those observed in other areas of the Great Lakes, with the exception of an increase in Oligochaeta density. Post-invasion (2002–03) shallow-water communities appear to be more homogeneous, dominated by zebra mussels and Isopoda, whereas deep-water sites are more heterogeneous due to the loss of Diporeia. Additional data on Diporeia density for several years between 1959 and 2004 indicated that current low densities are not typical of South Bay. Based on changes in the benthic communities and published literature on whitefish diets, we predict that unless whitefish are able to switch to Mysis as an alternative to Diporeia, post-invasion whitefish diets will only contain a maximum of 57 to 84% of their former energy content. These predictions are likely underestimates, as they do not take into account increased energy costs associated with reductions in total invertebrate density at historical foraging depths.