Because the Clean Water Act (CWA) prohibits discharges from unpermitted CAFOs, permit coverage (under the National Pollutant Discharge Elimination System, or NPDES) provides certainty to CAFO operators regarding activities and actions that are necessary to comply with the Clean Water Act. Compliance with the permit is deemed compliance with the CWA under section 402(k) and thus acts as a shield against EPA or state CWA enforcement or against citizen suits under section 505 of the CWA. Furthermore, NPDES permits for large CAFOs incorporate requirements (prescribed by the effluent limitations guideline) which allow for discharge when precipitation causes an overflow from a structure that is designed, constructed, operated, and maintained in accordance with the permit. Finally, upset provisions can afford permittees a defense when emergencies or natural disasters cause discharges beyond their reasonable control, as provided in federal regulation 40 CFR 122.41(n).
Under the CWA, operators who do not apply for permits operate at their own risk because any discharge from an unpermitted CAFO (other than agricultural stormwater; see #38328) is a violation of the CWA subject to enforcement action, including third-party citizen suits.
