Pathogens are tiny microorganisms that can cause diseases in people and animals. Examples of pathogens include viruses, bacteria, and parasites. People can get sick from pathogens by eating contaminatedshellfish such as shrimp or lobster. If pathogens contaminate an estuary, cities and towns will close beaches and shellfishing areas so people aren't allowed to use them. Pathogens find their way into estuaries through leaky septic systems, inadequately treated sewage, runoff from farms, pollution from boats and marinas, and waste from pets and wildlife.