With their position at the interface between land and ocean and their fragile nature, lagoons are sensitive to environmental change, and it is reasonable to expect these changes would be recorded in well-preserved taxa such as molluscs. To test this, the 4000-year history of molluscs in Great South Bay, a bar-built lagoon, was reconstructed from 24 vibracores. Using x-radiography to identify shell layers, faunal counts, shell condition, organic content, and sediment type were measured in 325 samples. Sample age was estimated by interpolating 40 radiocarbon dates. K-means cluster analysis identified three molluscan assemblages, corresponding to sand-associated and mud-associated groups, and the third associated with inlet areas. Redundancy and regression tree analyses indicated that significant transitions from the sand-associated to mud-associated assemblage occurred over large portions of the bay about 650 and 294 years bp. The first date corresponds to the transition from the Medieval Warm Period to the Little Ice Age; this change in climate reduced the frequency of strong storms, likely leading to reduced barrier island breaching, greater bay enclosure, and fine-grained sediment accumulation. The second date marks the initiation of clear cutting by European settlers, an activity that would have increased runoff of fine-grained material. The occurrence of the inlet assemblage in the western and eastern ends of the bay is consistent with a history of inlets in these areas, even though prior to Hurricane Sandy in 2012, no inlet was present in the eastern bay in almost 200 years. The mud dominant, Mulinia lateralis, is a bivalve often associated with environmental disturbances. Its increased frequency over the past 300 years suggests that disturbances are more common in the bay than in the past. Management activities maintaining the current barrier island state may be contributing to the sand-mud transition and to the bay's susceptibility to disturbances.