Understanding Water Quality Issues

Manure contains four primary contaminants that impact water quality: nitrogen, phosphorus, bacteria and other pathogens, and organic matter.


All living things require nitrogen, the fundamental building block of protein, for growth and survival. Livestock and poultry only use part of the protein in their feed rations for the production of meat or other animal products. The remaining protein is excreted as nitrogen in manure in the form of urea (in urine), and organic nitrogen (in feces).

When manure is applied to land, the soil’s aerobic environment converts common manure nitrogen forms to nitrate. Nitrate is highly soluble in water. When levels of residual nitrate become high and water moves through the soil profile, leaching can occur and cause contamination of water. There are several health concerns related to consumption of high-nitrate water. Infants and pregnant women are at greatest risk. Foremost is that nitrate contamination of drinking water restricts the oxygen in the bloodstream in infants under the age of six months, causing methemoglobinemia (blue baby syndrome). In addition, there are other less well-documented health impacts. The U.S. Environmental Protection Agency (EPA) has set a maximum contaminant level (MCL) of 10 parts per million (ppm) for nitrate in public water supplies.

Ammonium in surface water also represents an environmental risk to animals and wildlife. In most natural surface waters, total ammonium concentrations greater than 2 mg/l can be toxic to fish.

Ammonium and organic nitrogen forms found in manure are likely to be transported with surface water runoff and erosion. These forms of nitrogen are unlikely to leach through soils. In general, the filtering ability of soil restricts movement of organic compounds, and the negatively charged clay soil particles restrict the movement of positively charged ammonium. Ammonium can also be converted to ammonia and transported by volatilization and deposition processes. More about these processes is described in the nitrogen dynamics section.

Practice Question

Algae Boom in Lake Erie.

Phosphorus in surface waters can promote eutrophication.

Battling the Bloom: Lake Erie

Phosphorus is another nutrient that is essential for plant growth and development. It plays many critical functions, the primary one being the storage and transfer of energy through the plant. In confined livestock production systems, supplemental phosphorus is often essential for bone development and optimum animal performance. Commercially mined, phosphorus is a limited resource with approximately 40 years’ supply remaining in the United States. Thus, better use of manure phosphorus provides an increasingly important alternative to commercial fertilizers.

Phosphorus transported from agricultural lands to surface waters can promote eutrophication — an abnormal growth of algae and aquatic weeds in surface waters. Eutrophication is one of the leading water quality issues facing the nation’s lakes and reservoirs today. As this organic material decays, oxygen levels in the water decline, which can be detrimental to fish populations. Eutrophic surface waters may also experience blooms of cyanobacteria, which can kill livestock and pose health hazards to humans.

Phosphorus stored in soils is primarily fixed to soil minerals (iron, aluminum, and calcium) or to organic matter (living soil bacteria, crop residue, and partially decayed organic matter). Thus, soil erosion is the primary transport mechanism of particulate phosphorus to surface water.

Soil water also contains a small amount of dissolved phosphorus essential for plant uptake. Because the balance among the various phosphorus pools is heavily in favor of the organic and soil mineral forms, phosphorus leaching is rarely an issue. However, as soil phosphorus increases, phosphorus in runoff and erosion entering surface water become greater concerns.

Part I of Water Quality Issues | Part II - Pathogens and Organic Matter | Part III - Contaminant Pathways | Complete the Quiz


Sign up for updates from UNL Water

Sign Up Here