Levels of barium, cadmium, chromium, copper, mercury and vanadium were determined by plasma emission spectroscopy in sediments and oysters (Crassostrea virginica) in the Palizada, Chumpán and Candelaria rivers, which flow into the Términos Lagoon, state of Campeche, Mexico. The relation between the condition index of the oyster and the detected elements were determined as well. Significant relations were observed between copper (r = −0.825, p < 0.05) and chromium (r = −0.787, p < 0.05), which indicates the oysters’ affectation by ingesting both elements; concurrently, the results confirm that oysters present high tolerance to heavy metals. The average concentration of cadmium (2.05 μg/g), chromium (1.82 μg/g) and copper (115.55 μg/g) in rainy-season climate exceeded the limits for marine mollusks regarding different health standards. It was found that the rainy season, the sediment characteristics and organic matter content have a great influence on the transport and availability of heavy metals.