Field surveys in southeastern Raritan Bay and laboratory studies from 1999 to 2005 were conducted to compare the characteristics of mud and sand habitats in relation to the abundance of the northern quahog (Mercenaria mercenaria). In 2000, the population density of quahogs was about 15 times higher in the mud habitat than in the sand habitat. In addition, the mud habitat also had a dense population of the amphipod Ampelisca abdita (about 24,000 m⁻²) associated with it. This species produces mats of tubes over the bottom. The sediment surface of the mud was comprised mostly of fecal pellets, the majority of which was produced by A. abdita. In contrast, the sand habitat did not have A. abdita tubes or much erect surface structure; its sediments were comprised of medium grain sand (φ = 1.17–1.4). In southeastern Raritan Bay, the principal quahog predators are the longwrist hermit crab (Pagurus longicarpus), Atlantic oyster drill (Urosalpinx cinerea), and xanthid mud crabs. Collectively, they were >7 times more abundant in the sand habitat than in the mud habitat. We suggest that quahogs are abundant in the mud habitat because the presence of the tube mats probably reduces water siltation, encourages settlement of larval quahogs and deters predation on the quahogs.