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about Concentrated Animal Feeding Operations.
for a Wisconsin Pollutant Discharge Elimination System permit.
Contact information
Agricultural runoff management staff

Frequently asked questions Concentrated animal feeding operations WPDES permits

What is an “animal unit”?

“Animal units” (AU) measure equivalencies between animal types as established by s. NR 243.05, Wis. Adm. Code [exit DNR] and the CAFO WPDES permit program. For example, 1,000 beef cattle, 715 milking cows or 200,000 chickens are each equivalent to 1,000 AU. Livestock/poultry feeding operations with 1,000 or more AU are Concentrated Animal Feeding Operations (CAFO) and need a Wisconsin Pollutant Discharge Elimination System (WPDES) permit to operate.

The Animal Unit Calculation Worksheet [PDF], along with the Instructions [PDF], will help you determine the actual number of animal units in your operation.

What types of permits do existing, new or expanding livestock or poultry feeding operations need?

If you have, or will have a CAFO (livestock/poultry operation with 1,000 or more AUs), you must have a Wisconsin Pollutant Discharge Elimination System (WPDES) permit. The WPDES permit is a water quality protection permit designed to address manure and process wastewater handling at CAFOs.

In addition, other state and local permits might be necessary. Our State and Local Permit Checklist [PDF] is a good starting point to determine what additional permits you may need. The checklist doesn’t include every possible permit so check with your town, county, and state staff, too. Start early because permitting can be a long and complex process.

What happens if a permit expires?

Provided the permittee has submitted a timely reissuance application or notice of intent, the terms and conditions of their permit continue to apply until it has been reissued, revoked, or until an individual permit is issued for the discharge to which the general permit applied. See s. NR 227.51 Wis. Adm. Code [exit DNR] for additional information. A summary of expired CAFO permits is available here,

When will I need an approved WPDES permit for my livestock/poultry feeding operation?

You must have an approved CAFO WPDES permit before your operation reaches 1,000 animal units or more. The department requires that operations apply for the permit 12 months prior to becoming a CAFO. If your operation already has more than 1,000 animal units, but does not have a WPDES permit, please contact your regional DNR representative immediately.

What is the WPDES permitting process for a Concentrated Animal Feeding Operation (CAFO)?

You must submit a “preliminary” application at least 12 months before your operation plans to have 1,000 or more animal units. The preliminary application contains basic information about your operation. After the DNR receives your completed preliminary application, we conduct a site visit and provide you with information for your final application submittal.

At least six months before your operation will have 1,000 or more animal units, you must submit your “final” application. In your final application, you will provide more detailed information about your operation. You'll need to include design plans for proposed feed or manure storage structures, evaluations of existing manure and process wastewater storage and handling systems, and a nutrient management plan. Once the DNR determines your application is complete, we'll begin reviewing all submitted materials to determine if they comply with water quality protection requirements for CAFOs. Your application may also include a completed Environmental Assessment (EA) which serves to identify potential environmental, social and economic impacts of the proposed CAFO. As part of the permit issuance process, there is a public notice and comment period. During this comment period the permittee and members of the public can comment on the proposed conditions of the WPDES permit. In addition, the DNR may hold a public informational hearing on the permit (and EA) if it is warranted. Once the public comment period is complete and the DNR has responded to the comments, the DNR issues your final CAFO WPDES permit.

The WPDES Permit Application Process Flowchart [PDF] has additional information.

When should I submit my preliminary CAFO WPDES permit application?

A “preliminary” permit application must be submitted at least 12 months before an operator expects to reach 1,000 or more animal units. It is essential that you contact the DNR early on to ensure that permitting issues are addressed as part of the planning process and to be sure that the final permit is issued prior to actual construction or expansion. During the application process, regional DNR staff will make a site visit with you to gather information and further explain issuance procedures.

What should I include so my preliminary CAFO WPDES permit application is complete?

Please submit the following to the DNR CAFO intake specialist to ensure that your preliminary application is complete:

After I submit my completed application, what are the next steps?

The CAFO Intake Specialist sends the complete preliminary application to your DNR regional agriculture specialist. Approximately 30 days after your regional agriculture specialist receives the completed application, they will contact you to set up a site visit. The DNR regional agriculture specialist may make recommendations for revisions to your preliminary application based on the site visit. You will need to resubmit your revised preliminary application to make your final application complete.

When the intake specialist determines your application is complete, they distribute it to the appropriate regional agriculture specialist and Central Office reviewers. Please review the WPDES Permit Application Process Flowchart [PDF] for additional information.

What does my final WPDES permit application require?

Your final application for a CAFO WPDES permit should include:

The final CAFO WPDES permit contains requirements for proper runoff control, manure storage, and manure management. These requirements ensure no discharge of pollutants to navigable waters [PDF] and protection of groundwater.

After the DNR grants your CAFO WPDES permit, you must submit, to the DNR, a finalized Manure Management Plan (based on the conditions of the issued permit), a monitoring and inspection program, and annual reports summarizing manure landspreading. These requirements ensure permit compliance.

Every 5 years, CAFOs must submit a permit reissuance application for permit renewal. CAFOs must notify the DNR of any proposed construction or management changes.

May an existing or proposed CAFO begin construction of reviewable structures or systems before DNR approval of plans and specifications?

Before receiving approval for reviewable facilities and systems, you may construct buildings and other facilities that are not reviewable facilities and systems (i.e. animal housing, milking systems). You do this at your own risk. Construction without approval is a violation of s. NR 243.15, Wis. Adm. Code [exit DNR], and is a violation of the CAFO WPDES Permit. A proposed CAFO means an operation has submitted a WPDES permit application (complete or incomplete) and is subject to the same regulations as an existing CAFO.

The DNR strongly recommends you not begin any construction until we have completed an Environmental Analysis, if necessary, and issued an approval of plans and specifications for reviewable facilities and systems. Manure and process wastewater transfer systems are reviewable facilities, including any transfer systems associated with animal housing. Therefore, although animal housing itself is not reviewable, the animal housing design and location may depend on components that are subject to DNR review and approval.

What construction may an existing or proposed CAFO begin before the plans and specifications are approved?

Clearing, grubbing and rough grading are earth moving activities allowable per s. NR 108.03(2), Wis. Adm. Code [exit DNR] prior to approval of plans and specifications. Grubbing and grading activities include grading for site erosion control features, removing trees and stumps, stripping topsoil and constructing access roads. Placement of liner materials, concrete forms or fill materials for reviewable structures are not allowable earth moving activities.

Approval for burrow excavation is not necessary if it is to obtain fill for non–reviewable structures or systems, even if the excavation occurs where reviewable structures (ex: manure storage lagoon) will be located. If more than one acre will be disturbed, before beginning soil disturbance activities, you must have a valid WPDES stormwater construction site permit.

What types of CAFO projects require submittal of plans and specifications with DNR review and approval?

The CAFO Reviewable Facilities and Systems Checklist [PDF] lists the most common types of reviewable projects including:

  • existing facility evaluation;
  • runoff control;
  • manure storage: lagoon, digester or composting;
  • process wastewater storage (e.g., milking waste or egg wash);
  • manure transfer pipe, channel, reception tank or sand separation/storage;
  • feed storage area;
  • non-agricultural waste addition to storage or treatment systems, including digesters; and
  • closure/discontinuing use of a reviewable structure or system.

Additional information about project types is available in ch. NR 243 Wis. Adm. Code [exit DNR] and NRCS Standard 634 [PDF].

How long does it take to obtain DNR approval of plans and specifications?

It may take 45-90 days from receipt of your complete submittal for DNR approval of your plans and specifications. If a WPDES permit application or an Environmental Analysis (EA) is required, a longer approval time is necessary.

If a livestock or poultry operation intends to become a CAFO, but has not submitted an application for a CAFO WPDES Permit, can construction proceed without DNR approval?

It may be legal, but the DNR discourages this practice and owners should recognize they are taking significant extra risk. Prior to applying for a WPDES Permit, facilities and systems reviewable under ch. NR 243, Wis. Adm. Code, may be constructed without approval of plans and specifications, because the facilities and systems do not become subject to review until a WPDES Permit has been applied for (complete or incomplete).

The following related issues should be considered:

  • Ch. NR 243 Wis. Adm. Code [exit DNR] requires operations to submit an initial permit application 12 months before the increase in animals is expected.
  • Previously constructed facilities and systems (regardless of age) will be subject to engineering evaluation at the owner's expense and review by the DNR.
  • The owner may incur excess capital and operational costs to correct deficiencies caused by poor planning, particularly if the location or design doesn’t meet the code requirements and cannot be easily modified to meet those requirements.

The DNR advises owners to refrain from constructing facilities intended for expansion to become a CAFO until they have submitted a complete WPDES Permit application, including plans and specifications for new facilities and system, and have obtained written approval from DNR.

What level of Nutrient Management (NMP) planning is needed prior to applying for a WPDES Permit?

Final WPDES permit applications are considered complete only they include a complete and final Nutrient Management Plan. Please review the DNR's Nutrient Management Planning page for complete information.

Where can I find more information?

Please contact your regional DNR agricultural specialist for additional information

Last revised: Thursday May 23 2019