The Clean Water Act establishes a national pollution discharge elimination system to regulate operations that discharge pollutants directly into waters. Agricultural operations, including CAFOs, are covered. LPDD recommends that EPA strengthen its regulations in ways that would decrease GHG emissions incidentally to the water pollution controls at the heart of its mandate. For example, NPDES programs should prohibit CAFOs from spreading manure on frozen or saturated lands, insist on vegetated buffer zones along water courses, limit application rates, or require dry manure management, which can also reduce methane emissions.