The changes include the removal of the requirement that any large animal feeding operation that "proposes to discharge" pollutants into waters of the state--but does not actually discharge--obtain an NPDES permit. The changes were necessitated by the the 5th Circuit Court of Appeals' ruling earlier this year, National Pork Producers Council v. U.S. E.P.A. That case held that the "propose to discharge" threshold violated the Clean Water Act.
As a result of the National Pork case and IDEM's new NPDES regulations, the next few years will see many of Indiana's largest livestock farms leave the CAFO program and enter the state's confined feeding operation (CFO) program. The impact of those changes can be found in my earlier post: New Confined Feeding Operation Regulations Approved For Indiana Livestock and Poultry Farmers