Nitrifying bacteria can oxidize ammonium to nitrite (NO2-) and then to nitrate (NO3-). Nitrite is toxic to most fish and other aquatic species, but it typically does not accumulate in the environment because it is rapidly transformed to nitrate in an aerobic environment. Alternatively, nitrite (and nitrate) can undergo bacterial denitrification in an anoxic environment. In denitrification, nitrate is converted to nitrite, and then further converted to gaseous forms of nitrogen - elemental nitrogen (N2), nitrous oxide (N2O), nitric oxide (NO), and/or other nitrogen oxide (NOx) compounds. Nitrification occurs readily in the aerobic environments of receiving streams and dry soils while denitrification can be significant in anoxic bottom waters and saturated soils.
Nitrate is a useful form of nitrogen because it is biologically available to plants and is therefore a valuable fertilizer. However, excessive levels of nitrate in drinking water can produce negative health impacts on infant humans and animals. Nitrate poisoning affects infants by reducing the oxygen-carrying capacity of the blood. The resulting oxygen starvation can be fatal. Nitrate poisoning, or methemoglobinemia, is commonly referred to as "blue baby syndrome" because the lack of oxygen can cause the skin to appear bluish in color. To protect human health, EPA has set a drinking water Maximum Contaminant Level (MCL) of 10 mg/l for nitrate-nitrogen. Once a water source is contaminated, the costs of protecting consumers from nitrate exposure can be significant. Nitrate is not removed by conventional drinking water treatment processes; its removal requires additional, relatively expensive treatment units.
Nitrogen in livestock manure is almost always in the organic, ammonia or ammonium form but may become oxidized to nitrate after being diluted. It can reach surface waters via direct discharge of animal wastes. Lagoon leachate and land-applied manure can also contribute nitrogen to surface and groundwaters. Nitrate is water soluble and moves freely through most soils. Nitrate contributions to surface water from agriculture are primarily from groundwater connections and other subsurface flows rather than overland runoff (Follett, 1995).