Mangrove Lagoon, located on the island of St. Croix, US Virgin Islands (USVI), is one of few actively bioluminescent lagoons in a location experiencing significant anthropogenic impacts. The bioluminescence is due to an abundance of the dinoflagellate Pyrodinium bahamense in the water column. We recovered surface sediments and sediment cores from Mangrove Lagoon to analyze the spatial distribution and temporal variability of P. bahamense cysts in this system. Surface sediment P. bahamense cyst concentrations ranged from 0 to 466 cysts g −1 dry sediment, with higher abundances associated with elevated surface water nutrient concentrations and a mixed terrestrial-marine organic matter source regime. In combination with available bioassay data, we hypothesize that phytoplankton utilize nutrients rapidly and subsequent decay of organic matter makes nutrients available for dinoflagellates at the sediment-water interface in the eastern and northern quadrants of the lagoon. However, the nutrients are rapidly exhausted during counterclockwise lagoon circulation resulting in the decline of primary productivity and dinoflagellate abundance in the western quadrants. Downcore profiles suggest that P. bahamense blooms have been occurring for decades, declining in recent years. No cysts were present in sediments predating dredging activities of the 1960s that created Mangrove Lagoon. Recent reductions in cyst abundance may be the result of limited primary productivity caused by restricted water exchange with Salt River Bay due to shallowing of a sill at the mouth of the lagoon. This research highlights the need for more comprehensive geochemical and fossil analyses to better understand long-term ecological variability and inform conservation efforts of these unique habitats.