Farmers collect liquid manure in catchment ponds or lagoons where it can be degraded by anaerobic bacteria , sunlight, and water. Anaerobic bacteria promote the decomposition of carbon-containing compounds into carbon dioxide and methane, as well as nitrogen into ammonia and ammonium. Bacteria and other microorganisms are filtered out by the soil, but can enter surface water resources in run-off if waste application rates are high and the soil becomes saturated. Saturation of soil can also contribute to contamination of ground water sources. Contamination may result if waste water is applied to fields located adjacent to a stream or lake.
Contamination also occurs when lagoons leak.
Often, agricultural regions depend upon sunken private wells for drinking water, and since federal regulations do not require monitoring of private wells, it is up to the owner or user to test thier drinking water. There are many protective practices that can can be employed in order to decrease the possibility of water contamination from animal wastes. Divert runoff from land above the barnyard, and divert barnyard runoff away from streams and ponds. Create a riparian buffer zone by lining the lagoon with trees and vegetation. This will provide a rich source of soil microbes which degrade and consume nutrients such as nitrate and phosphorus found in manure.