Aquaculture of the northern quahog (=hard clam) Mercenaria mercenaria (Linnaeus, 1758) is widespread in shallow waters of the United States from Cape Cod to the eastern Gulf of Mexico. Grow-out practices generally involve bottom planting and the use of predator exclusion mesh. Both the extent and scale of clam farms have increased in recent decades resulting in concerns regarding the impacts of these practices on estuarine fauna. Seasonal distribution, abundance, biomass, species richness, and community composition of nektonic, demersal, epibenthic, and infaunal organisms were examined in cultivated and uncultivated shallow-water habitats in Virginia and New Jersey. The results reveal that clam aquaculture, as practiced in both Virginia and New Jersey, has remarkably few quantifiable impacts on estuarine fauna. Seasonal variations were observed in the biota, but of the 39 population and community metrics tested, mean values associated with 26 did not differ between cultivated and uncultivated areas, 5 had decreases and 8 had increases. For recently harvested areas, 32 of 39 variables were not different from uncultivated areas, 6 decreased in at least one season, and 1, blue crab biomass, had a marginal increase. Decreases were observed in the abundance and biomass of infauna (exclusive of the cultured clams) on clam farms, including in harvested areas, relative to natural uncultivated areas. This was accompanied, however, by substantial increases in epibenthic macroalgae, which in some cases supported increased epifaunal species richness and abundance relative to uncultivated areas. Habitat use by finfish, crustaceans, and terrapins was largely unaffected by the presence of clam farms.