The Caloosahatchee Estuary has been exhibiting signs of impaired ecological health due to the extensive hydrological alteration, agricultural land use, and increasing watershed development. This project investigated the responses of the American oyster, Crassostrea virginica at five locations in the Caloosahatchee River in relation to salinity changes, levels of heavy metals, pesticides, and PCBs in the water as well as in the oyster tissue. Individual heavy metal and organochlorine pesticide concentrations in oysters varied significantly between sampling locations and sampling months. PCB concentrations in oyster tissues were below detection limits as were the metal, pesticide and PCB concentrations in water at all the sampling locations. Both heavy metal and pesticide concentrations decreased with increasing distance downstream indicating upstream source of contaminants. The highly pathogenic oyster parasite Perkinsus marinus infection intensity (level) and prevalence (% infected oysters), condition index, spat recruitment, and gonadal index showed a seasonal trend varying with spawning activity and increased downstream. However, juvenile oyster growth was higher at upstream estuarine locations. Oyster responses varied more with seasonal programming (salinity), rather than due to contaminant levels. While significant correlations were noted between some oyster responses and metal concentrations in oyster tissues, overall metal concentrations were low compared to national averages. It appears that oyster health in the Caloosahatchee River is influenced more by freshwater inflow and resulting salinity fluctuations, rather than due to the measured contaminants.