For a permitted AFO/CAFO (some states maintain AFO permits) inspections will focus on compliance with the permit provisions. Items of primary concern will likely be: manure storage structure integrity and level records (freeboard), records of any discharges, land application records that reflect the Nutrient Management Plan (NMP), nutrient export records and physical evidence related to the previously described records. A variety of other issues or permit provisions will likely be addressed by inspectors, but primary concern will be those that demonstrate water quality has been protected through management defined by the permit and NMP. For non-permitted operations, there are no required records or management plans to verify, so inspections will largely be based on physical evidence of discharges such as over-application, over-topped or leaking storages, animal's direct access to surface water in confinement, or observable environmental damage.

-Thomas Bass, Montana State University