The guidance seeks to clarify which CAFOs have a "duty to apply" for a National Pollutant Discharge Elimination System permit under the final 2008 CAFO rule. A federal appellate court ruling in 2005 in the Waterkeepers case found that CAFOs that do not discharge nor propose to discharge were not obliged to seek a permit.
www.epa.gov/npdes/pubs/cafo_implementation_guidance.pdf