The impact of Dreissena (Dreissena polymorpha and D. bugensis) on the benthic bacterial community in lakes is largely unknown. Therefore, we quantified differences in the structure and activity of bacterial communities living in sediments (1) associated with Dreissena clusters, and (2) unassociated with established clusters (lake bottom sediments). Dreissena clusters and sediments were collected from locations in Lake Erie, Lake Ontario, and several inland lakes. Denaturing gradient gel electrophoresis (DGGE) analysis of the benthic bacterial community showed that the bacterial populations selected for by Dreissena represent a subset of the bottom communities and are geographically distinct. Community-level physiological profiling (CLPP) showed that overall bacterial activity and metabolic diversity were enhanced by the presence of clusters in all samples, with the exception of those harvested from the two Lake Erie sites. Therefore, Dreissena appears to affect both structure and metabolic function of the benthic bacterial community and may have yet unexplored ecosystem and food web consequences.