In the process of investigating the cause of the transmission of botulism to the pelicans, some dying fish were collected and sampled by the U.S. Fish and Wildlife Service. These fish were analyzed by the Northwest Biological Science Center in Seattle and the Vibrio Alginolyticus bacteria were found to exist in them. These bacteria are common in salt water species. Tunas, mahi mahi, bluefish, sardines, amberjack, and mackerel are often found with Vibrio bacteria. Vibrio kills the fish it infects.

It is theorized that, as the Tilapia were dying because of the bacteria, their bodies became host to the botulism virus. Botulism requires an anaerobic environment to survive. Because of this, normal healthy fish cannot support the virus. As the fish weakened and, shortly before their death, their bodies offered conducive conditions for the virus. Pelicans (as all predators) find it easier to hunt disabled prey. The theory continues to suggest that some pelicans caught and ingested the dying Tilapia that now contained the virus, and thus became ill themselves.

Botulism outbreaks occur in late summer because water temperatures are greater. As the water cools, the virus is less active. Avian botulism is very common worldwide; it is not endemic to the Salton Sea, and in itself doesn't reflect a decline in the Sea's systems. This class "C" botulism is not a threat to human health.

The Vibrio bacteria is also very common in saltwater environments. Commercially caught and processed fish are recognized to contain this bacteria. However, it is not considered a health threat when the fish are cooked or processed and not allowed to spoil prior to processing. Health departments say that eating fish from the Sea is safe as long as they are not eaten raw, and they are not allowed to spoil before being processed. Cooking the fish destroys the bacteria. Keeping the fish on ice after they are caught prevents them from spoiling.