First-time CAFO WPDES permit applications

If your operation has 1,000 animal units (AU), your operation is a Concentrated Animal Feeding Operation (CAFO) and you must obtain a Wisconsin Pollutant Discharge Elimination Permit (WPDES) from the Department of Natural Resources.

WPDES permit applications

• WPDES permit requirements
• Application materials, instructions and guidance
• Detailed instructions for first time applications [PDF]

Preliminary and final applications must be submitted online through the DNR’s Water ePermitting System. The ePermitting System includes all required forms.

Instructions to submit your application using the ePermitting System: CAFO ePermitting User Guide

Application timeline, process and requirements

For an overview of the permit application timeline and process, review the CAFO WPDES application process flowchart [PDF].

Note: Materials denoted with an asterisk (*) are available in the ePermitting System.

1. Preliminary application

If you are applying for a CAFO WPDES permit for the first time a preliminary permit application must be submitted at least 12 months before your CAFO proposes to begin operating. Preliminary application components include the following items.

• Form 3400-025 Livestock/Poultry Operation WPDES Permit Application (*)
• Form 3400-025A Animal Unit Calculation Worksheet [PDF] (*)
• Aerial maps showing the features and structures of each site which is part of the CAFO (To create your maps, you may use the DNR Surface Water Data Viewer)

You must submit a preliminary application prior to submitting a final application. For first time issuances, the ePermitting System will not allow submittal of a final application until a preliminary application has been submitted. Your preliminary application materials will include owner contact information and detailed site information. The site information is required for every site your farm owns or manages, where animals are kept, and that share feed storage, manure storage, or acreage for manure land application. Animal unit calculations and site maps are also required for each site. The site maps must clearly delineate existing and proposed structures and systems.

Within 30 days of receiving your preliminary application, your specialist will set up a site visit with you. After the site visit, the specialist will send you a letter listing your final application needs and whether your operation is eligible for a general or individual permit.

2. Final application

After submittal of your preliminary application to the DNR, you must submit your final permit application at least six months before your CAFO proposes to begin operating. Final application components include the following items.

• Forms 3400-025 and 3400-025A and the maps submitted for your preliminary application
• Environmental Analysis Questionnaire [PDF] (if required)
• Form 3400-025B Nutrient Management Plan (NMP) Checklist (*)
• NRCS 590 Nutrient Management Plan Checklist [PDF]
• Five-year Nutrient Management Plan
• 180-day manure storage calculations [XLS] and supporting documentation
• Reviewable facilities checklist form 3400–025C (if plans & specifications or evaluations are being submitted) (*)
• Plans & specifications for reviewable structures and systems (if proposed)

The DNR’s Permit FAQ will provide additional answers to your questions about application components.

Consultants and other permits

The department strongly recommends you hire water engineer consultants to help you complete the required forms.

Besides the WPDES Permit, there are normally other permits and approvals required for new or expanding dairies and other animal feeding operations. You will need to ask your local, county and state officials directly to get information about these other permits and authorizations.

Submittal information

At least 12 months before your operation becomes a CAFO, submit your preliminary application to the DNR through the ePermitting System.

No later than 6 months after the DNR determines your preliminary application complete, submit your final application to the DNR through the ePermitting System.