Historic human-imposed tidal flow restrictions at many New England estuaries have resulted in dramatic alteration of estuarine community structure and function. East Harbor, a 291-ha coastal lagoon and salt marsh in Truro, Massachusetts, was artificially isolated from Cape Cod Bay in 1868. After the isolation, salinity decreased to near freshwater levels, and estuarine fish and invertebrate populations declined precipitously. Partial tidal flow was restored to East Harbor in 2002; since then, East Harbor has experienced substantial increases in salinity, and native fauna has begun to return to the system. The objective of this study was to obtain information on marine molluscan populations recolonizing East Harbor. Using a combination of benthic cores and direct searching, we surveyed 50 plots throughout the estuary in July and August 2005. We detected 16 molluscan species in East Harbor as a whole; the four most abundant species were Mya arenaria, Littorina spp., Mytilus edulis, and Mercenaria mercenaria. We found significant differences in species richness and abundance of these species among three regions of East Harbor that varied markedly in salinity and distance to Cape Cod Bay; diversity and abundance were both highest in Moon Pond, which has a direct connection with sources of seawater and marine biota, and lowest in the northwest cove, which receives high freshwater discharge. These findings demonstrate the effectiveness of Cape Cod National Seashore’s preliminary tidal restoration efforts while underscoring the continued need for full tidal restoration at East Harbor and other tide-restricted estuaries.