Overharvest of the once highly abundant northern quahog, or hard clam [Mercenaria mercenaria (Linnaeus, 1758)], has decimated local populations on Long Island, NY, and the ecosystem services they provide. Among the potential ecological consequences of the loss of hard clams, impacts on benthic community structure and function have not been well documented. This study took advantage of a large-scale hard clam restoration effort by The Nature Conservancy in Great South Bay, NY, to investigate these parameters. The benthic communities between areas planted with high densities of adult clams (i.e., spawner sanctuaries) and adjacent sites with no transplants were compared. In clam-stocked areas, there were greater trophic and taxonomic group densities, especially for some environmentally sensitive groups such as crustaceans, and increased species richness, which in turn altered community structure of the resident infauna. Differences between paired sites for macrofaunal diversity and community structure were also observed, likely reflecting larger scale differences in invertebrate communities. Minimal differences were observed in sediment porosity, carbon and nitrogen content, and total organic matter between adjacent areas with and without clams, although all of these parameters were significantly associated with community structure. Although shell density was significantly higher in clam-stocked plots, it explained little of the variation in macrofaunal composition on its own or in combination with other environmental parameters, but in combination with the living clams may have added enough environmental complexity to enhance densities of different trophic groups. Within the short period of 3 y, differences in the benthic community with the presence versus the absence of clams were already detectable. More long-term data incorporating the effect of processes at multiple scales are needed to gain insight into the complexity of rehabilitating coastal benthic environments following the removal of important species such as clams. The results of this work support the notion that M. mercenaria acts as an ecosystem engineer, modifying the environment by creating habitat and enhancing the abundance of other species.