EPA Definitions of AFOs and CAFOs: 

"An Animal Feeding Operation (AFO) is a facility in which livestock or poultry are raised or housed in confinement, and where the following conditions are met: (1) animals are confined or maintained for a total of 45 days or more in any 12-month period, and (2) crops are not sustained in the normal growing season over any portion of the lot or facility (i.e., animals are not maintained in a pasture or on rangeland)."

"Concentrated Animal Feeding Operations (CAFOs) are a subset of AFOs. In addition to meeting the above conditions, an AFO is a defined as a CAFO if it meets minimum size thresholds (AFOs with more than 1,000 animals are CAFOs; those with 300-999 animals may be CAFOs, depending on discharge characteristics; and those with fewer than 300 may be CAFOs in some cases) and either one of these conditions: (1) pollutants are discharged into navigable waters through a manmade ditch or similar manmade device, or (2) pollutants are discharged directly into waters of the United States that originate outside of and pass over, across, or through the facility, or otherwise come into direct contact with the confined animals."

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The Clean Water Act defined CAFOs as a "point source pollutant." This act states that an EPA or “qualified state” issued permit is necessary for drainage of pollutants from “point sources,” otherwise it is strictly prohibited. Up until 2003, the only regulations for these operations where the guidelines the Clean Water Act had enacted in 1972.

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In 2003 there were many long-overdue updates to the past requirements of CAFOs. Waste discharge and permit requirements were among the subject matters that were modified. For the first time it was required that all Condensed Animal Feeding Operations must apply for a permit in order to discharge waste, and secondly to develop/apply a plan for nutrient management. These newly created regulations were a step in the right direction, but the court case, “Waterkeeper Alliance et al. V. EPA,” in 2005 challenged some of these newly required regulations. This resulted in the EPA significantly changing their guidelines, by completely eliminating their “duty to apply” regulation, that required all CAFOs must either prove that they have no potential discharge, or apply for a discharge permit if it is known that the operation will discharge. A part of the 2003 ruling that was maintained was the agricultural storm water discharge exemption. Environmental groups explained that the ruling had left much of the original ruling still in place, yet the EPA chose to dramatically revise their original 2003 rule. 

Something worth noting is that NMPs are not actually enforceable parts of the permit requirement, which was confirmed in the 2008 rule. This rule once again clarified the controversial "duty to apply" rule. Lastly, in 2014 and 2016 there have been vague clarifications that have updated the CWA.