Puerto Mosquito is a bioluminescent bay located on the southern shore of Vieques, Puerto Rico. It is a shallow bay (<5m) surrounded by mangroves with a narrow mouth that leaves it subjected to little flushing and thus an excellent habitat for dense populations of the bioluminescent dinoflagellate Pyrodinium bahamense var. bahamense. Puerto Mosquito faces multiple dangers: possible contamination from the practices and waste products of the United States military on nearby land, siltation from increased erosion due to upslope building, and the possibility of increasing future tourism when the military is scheduled to depart in 2004. To our knowledge no other geologic work has previously been conducted within Puerto Mosquito. A transect of grab samples and a 1.1 meter core were used for grain size analysis. The core displays a boundary between marine and terrigenous material at a depth of 35-40cm. Calcium carbonate within the samples was measured to determine productivity levels. The size distribution of the fine (<63μ) fraction was measured to determine relative current strength. Clostridium perfringens were counted to assess the influx of human fecal material, and trace element concentrations were analyzed. Using the 1.1m core a temporal distribution of trace elements was derived, indicating which elements have only recently been increasing and whether they are increasing throughout the bay or are concentrated in the areas closest to the mouth. Concentrations of arsenic have reached unnormalized levels of up to 12ppm. Individual particles in the coarse fraction (63μ-1mm) were counted to assess changes in the microorganisms and variances in the terrigenous component. Ostracods were counted and used as indicators of environmental conditions; species diversity preliminarily decreased in the northwestern corner of the bay and then dramatically increased approaching the mouth of the bay. Measurements of dissolved oxygen, pH, temperature and salinity were taken to correlate changes in ostracod abundance to changes in water conditions. This project was designed to determine, through spatial and temporal analysis, baseline data that can be used to monitor future changes within this rare and fragile ecosystem as well as determine any that may have already taken place due to anthropogenic factors.