Here is a collection of articles about the NPDES permit as defined by the Federal EPA.  This permit is administered by IDEM for CAFOs.

http://cfpub.epa.gov/npdes/afo/caforulechanges.cfm

http://cfpub.epa.gov/npdes/home.cfm?program_id=7

http://cfpub.epa.gov/npdes/whatsnew.cfm?program_id=7

http://cfpub.epa.gov/npdes/faqs.cfm?program_id=7

http://cfpub.epa.gov/npdes/pubs.cfm?program_id=7