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Water quality permits for CAFOS

The DNR has issued a Wisconsin Pollutant Discharge Elimination System (WPDES) general permit for large dairy Concentrated Animal Feeding Operations (CAFOs) with 1,000 to 5,720 animal units (AU). A WPDES individual permit is still required for dairy CAFOs with more than 5,720 animal units and all non-dairy (swine, beef, poultry, etc.) CAFOs with more than 1,000 animal units.

General permit

Application process and requirements

The individual WPDES permit application requires an environmental review that is not required for the general permit. The rest of the application process, materials and level of DNR review are essentially the same for general or individual WPDES permit types.


The WPDES general permit is limited to dairy CAFOs with a record of compliance in protecting good water quality and meeting the following size or status requirements:

  • new or expanding dairy operations reaching or exceeding the 1,000 AU threshold for the first time, but not planning to expand beyond 5,720 AU;
  • currently permitted dairy operations with 5,720 animal units or less; or
  • currently permitted dairy operations expanding to 5,720 AU or below; and
  • at least 80 percent of the operation's AU falls under the dairy animal type.

Large dairy CAFO WPDES general permit

Small and medium CAFO WPDES general permit

The DNR is working on the development of a general WPDES permit for animal feeding operations with fewer than 1,000 animal units that fail to manage water quality impacts. No date has been set for a decision on the issuance of that general permit and the public comment period has closed.