The primary water quality concern with feedlots is managing animal manure.
Animal manure is a useful resource when properly used as fertilizer.
However, when improperly stored, handled and disposed of, nutrients from manure can contaminate groundwater and surface water. In surface water, this can lead to increased algae and plant growth, oxygen depletion, toxicity and the presence of disease-causing organisms. In groundwater, nitrates and pathogens can cause negative human and animal health effects. Since 1971, the MPCA has been responsible for issuing feedlot permits to owners that have submitted applications. In 1978, Certificates of Compliance and interim permits replaced the SW-A permits.