Nitrates exist in the environment in a variety of forms. Nitrate forms found in streams and lakes are important nutrients for aquatic life. Natural nitrate levels in streams are very low, usually below 5 mg/L (in non-agricultural areas). Inputs from point and nonpoint sources dramatically increase nitrate levels in streams. Nitrate is carried through the water to streams and ditches primarily through subsurface flow (tile) and overland flow. Subsurface flow, particularly tile, yields the highest loss of nitrate from agricultural fields. As water drains through subsurface tile it picks up nitrate from the soil. Thus, tile water is usually much higher in nitrate concentration than in water from overland flow.

The predominant form of nitrogen in Minnesota River basin streams is nitrate. Like phosphorus, nitrate can stimulate excessive levels of algal growth in streams. In recent years, this problem has been particularly severe in the Gulf of Mexico where development of a hypoxic zone (hypoxia means "low oxygen) has been linked to elevated nitrate levels carried to the Gulf by the Mississippi River. Reduced oxygen levels in the hypoxic zone, brought on by decomposition of algae, have damaged the shellfish industry and continue to threaten the aquatic ecosystem of the Gulf Region. The Minnesota River has been identified as a substantial contributor of excess nitrate to the Mississippi River and the Gulf Region. In addition to over-stimulation of algae, elevated levels of nitrate in drinking water can cause methemoglobinemia, or blue-baby syndrome (State of the Minnesota River Water Quality Summary 2000-2005).