Scientists and environmental managers break pollution into two categories: point source and nonpoint source pollution. Direct contamination of waterways, such as industrial waste pouring from a factory drain into a river, is an example of point source pollution. Pollutants such as motor oil leaked on parking lots, plastic grocery bags, pesticides, fertilizers, detergents, and sediments are known as nonpoint source pollutants.

Stormwater runoff from nonpoint source pollution is one of the most significant threats to aquatic ecosystems in the United States. As water runs over and through the watershed, it picks up and carries contaminants and soil. If untreated, these pollutants wash directly into waterways carried by runoff from rain and snowmelt. These contaminants can infiltrate groundwater and concentrate in streams and rivers, ultimately being carried down the watershed and into the ocean. Nonpoint source pollution is linked to the formation of large dead zones (areas with minimal oxygen) in the ocean and also threatens coral reef ecosystems around the world.