Estuaries are dynamic environments that provide vital habitat to ecologically and commercially important bivalves. In some cases, freshwater tributaries can introduce cyanobacteria and associated cyanotoxins into estuaries that may subsequently accumulate in estuarine bivalves. Temporarily open/closed estuaries (TOCEs), which only experience tidal input for limited periods of time, may be particularly vulnerable to the accumulation of cyanotoxins in bivalves as they can be subject to freshwater input without tidal flushing and may experience lower salinities and cyanobacterial blooms. This study quantified levels of microcystin in bivalves collected as a time series over a five-year period (2017-2021) from Mecox Bay, a TOCE on Long Island, NY, USA, that hosts a productive oyster fishery and is downstream of a freshwater body that hosts microcystin-producing cyanobacterial blooms. During the study, microcystin was detected in all bivalves monitored including Eastern oysters (Crassostrea virginica), blue mussels (Mytilus edulis), and soft-shell clams (Mya arenaria), with levels in oysters exceeding those in other species and frequently exceeding 10 ng g