Pathogens are disease-causing organisms. They include bacteria, viruses and other parasites. Pathogens pose a major health threat to people who swim, fish, or boat in estuaries, as well as to filter-feeding animals, like oysters, mussels and clams. These animals concentrate the pathogens in their tissues, making them dangerous for humans to eat.
Pathogens can come from many sources, including sewage treatment plants, leaky septic systems, pet, livestock, or wildlife wastes, and combined sewage overflows (CSOs). CSOs are probably the largest contributor of bacteria and viruses in most estuaries. They carry the combined sewage from residential, industrial and commercial wastes in the form of sewage solids, metals, oils, grease and bacteria. During heavy rains, CSOs combine with storm water and overwhelm sewage treatment plants. The result is that untreated or partially treated waste flows directly into the estuary.
Contamination by pathogens can result in the temporary or permanent closure of beaches and shellfishing areas. In some cases, health officials may warn citizens that they should restrict the amount of fish and shellfish that they eat.