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The Environmental Integrity Project, Inc. (EIP), Iowa Citizens for Community Improvement (ICCI) and the Iowa Chapter of the Sierra Club submits comments to EPA on its Clean Water Act rule for CAFOs asking the Agency to (1) establish a regulatory presumption that Large CAFOs actually discharge and designate certain categories of CAFOs to be proposed dischargers; (2) require a CAFO to be in compliance with a nutrient management plan (NMP) that is incorporated into a federal National Pollutant Discharge Elimination System (NPDES) permit before it can qualify for the agricultural stormwater exemption; (3) eliminate the general permit process for CAFOs so that NMPs are incorporated into individual permits after public review and opportunity for a hearing; (4) require that all elements of an NMP be incorporated into an NPDES permit; (5) clarify that water quality based effluent limitations apply to new sources of swine, veal and poultry operations, and (6) issue a new determination that identifies BCT technologies that achieve greater fecal coliform reductions than achieved by the BPT technologies identified in the 2003 Final Rule.