During the summers of 1981 and 1982, studies were conducted at Jamaica Bay Wildlife Refuge, Long Island, New York, to determine whether annual water-level drawdowns used to create shorebird habitat also led to the occurrence of avian botulism (Clostridium botulinum type C). Low levels of morbidity and mortality from avian botulism occurred on the two ponds throughout both summers, but there was no apparent relationship between the occurrence or rates of botulism losses and drawdowns of the ponds. Botulism also occurred throughout both summers on other areas of the refuge. Botulinal toxin was found in fly larvae associated with avian carcasses, including birds that did not die from botulism. Toxin was not found in other samples of aquatic biota in the ponds, although it was demonstrated in a single sample of decomposing sea lettuce (Ulva lactuca) in Jamaica Bay. Aspergillosis (Aspergillus fumigatus) and salmonellosis (Salmonella spp.) were also frequently-diagnosed causes of morbidity and mortality. We believe that botulinal toxin present in carcasses of birds dying from botulism, or produced postmortem in birds dying from other causes, on the two ponds and other areas in Jamaica Bay were a major source of botulinal toxin. Toxin could be ingested by birds through direct scavenging on carcasses, or by consumption of toxic fly larvae associated with carcasses. Diligent carcass pickup at the two ponds is recommended to reduce mortality from avian botulism.