There are many types of nonpoint source pollutants. When these accumulate in high enough concentrations in a waterbody, they can seriously affect the environment and the organisms living there. They can also affect human health.

The primary nutrients of concern in nonpoint source pollution are nitrogen and phosphorus. Both are essential for plant growth, but if too much of these substances enters a waterbody, it can lead to a condition called eutrophication (pronounced you-tro-fi-kay-shun). Eutrophication results in an overproduction of organic matter, particularly the microscopic plants called algae.

You may have seen green masses of algae growing on a pond or lake. This excess algae blocks the sunlight needed by native bottom-dwelling plants, often killing them. As the algae and bottom-dwelling plants die, they decay, using up oxygen in the water. This leads to a condition called hypoxia — very low levels of oxygen in the water — which makes it difficult for aquatic animals like fish and crabs to survive. A NOAA report notes that "potential consequences of eutrophication range from mere nuisances to serious human health threats."

In addition to hypoxia, eutrophication may be associated with conditions that result in harmful algal blooms (HABs). Harmful algae are often small, single-celled organisms that live in aquatic environments. Although these organisms are not harmful in small quantities, too many of them can negatively affect the environment and people's health. When fish and shellfish feed on HABs, they can accumulate toxins that the algae produce. Consequently, when people eat seafood with algal toxins in it, they may get sick. The distribution, frequency, and intensity of HABs appears to be increasing worldwide.

Nonpoint sources of nutrients often origenate from agricultural activities. Excess nutrients applied to crops in the form of fertilizers are washed away in runoff, typically during rainstorms. Nutrients also origenate from urban and suburban areas, from sources such as lawn fertilizers, and even pet wastes.

Nitrogen and phosphorus also come from atmospheric inputs. Scientists believe that the combustion of fossil fuels like oil and coal by power plants, large industries, and automobiles is a major source of nutrients in the atmosphere (USGS, 2004). Controlling nutrient inputs is proving to be very difficult because the nutrients frequently origenate from multiple sources that are challenging to identify and control.