CAFOs Plan Ahead: Three Programs You Need To Know About

Keeping your improvement projects on schedule means getting your product to market quicker and more efficiently.

Are you planning an important project?

An improvement project means you may have multiple permits which require your attention and compliance. If your improvement project falls into one of these examples below, plan ahead to comply with permitting processes— it’s a planning step that will save you time and money in the long run.

These types of structures and systems require permitting prior to construction:

  • Manure storage facilities
  • Runoff control structures
  • Manure treatment or transfer systems, including those related to animal housing
  • Digesters for biogas production
  • Permanent spray irrigation or other land application systems
  • Groundwater monitoring systems
  • Compost facilities
  • Feed and other raw materials storage
  • Other structures or systems associated with the storage, containment, treatment, or handling of manure or process wastewater.

1) Wisconsin DNR Wetland Permitting Process

As of June 1, 2016, you must incorporate a pre-application review process under the changed WDNR Wetland Delineation and Screening Policy. If the screening process reveals your project has the potential to impact wetlands, you will need extra time for a wetland delineation. Your delineation will also need WDNR concurrence before you can apply for a permit.


Property owners seeking permits for concentrated animal feeding operations will need to review available maps to determine if wetlands are on, or next to, a proposed project. While this new process may speed up permitting for some projects, it means significant pre-planning. Field work, including the boundary reviews by regulatory agencies, must be conducted during the growing season, which typically is between April and October.

Finally, know that WDNR concurrence may take up to 60 days. If you are planning a project to begin next spring, your delineations should be completed by August 2016 to give the WDNR adequate time for review.


Simply, anyone proposing a project. Specifically, the list of affected projects includes:

  • Any project disturbing wetlands.
  • Any project requiring a Stormwater Permit (if disturbing more than one acre of land).
  • New or expanded concentrated animal feeding operations.


The pre-screening process requires you look at a variety of maps. The WDNR recommends using their Surface Water Data or local GIS sites. If the maps show wetlands might be present on or next to a project, you will need to get a wetland review from a qualified wetland professional.

A map of Devil’s Lake State Park with wetland inventory (gold) and the the wetland indicators (pink) layers. Projects on or adjacent to either gold or pink layers will need a pre-screening. (Source:


  • A wetland review includes either of the following:
  • A wetland determination report identifies the absence of wetlands on or adjacent to the project site
  • A wetland delineation report defines the boundaries of the wetlands

Reports must be submitted to the WDNR, the US Army Corps of Engineers or both, and must be approved by one of these agencies before applying for a permit. Finally, documentation of approval must be included in the permit application.


The goal of the new WDNR wetland permitting policy is to:

  • Reduce permitting delays
  • Improve diligence to identify wetlands
  • Provide a consistent statewide process for determining a project’s potential to impact wetlands.

2) Wisconsin Pollutant Discharge Elimination (WPDES) Permit

For the WPDES program, you must plan ahead. At least 90 days before beginning construction, existing or proposed CAFOs must submit plans and specifications for reviewable construction projects to the WDNR for approval. Approval of plans and specifications is a requirement before proceeding with construction.

3) Natural Resources Conservation Service

NRCS standards define the practice (project) and where it applies. Practice standards are detailed requirements for installing the practice in the state. Technical standards are the primary scientific references for NRCS. They contain technical information about the conservation of soil, water, air and related plant and animal resources.

One challenge is the state technical standards continually change to meet Federal EPA rules, making a review an important step in the process. In fact, changes are under way now. SEH is participating in a work group with the WDNR, NRCS and DATCP to revise technical standards for Vegetated Treatment Areas to enhance the protection of the surface and groundwaters of the state. This means changes may occur to comply with the recently released (Sept. 2015) National 635 standard. CAFOs need to meet EPA's effluent guideline of no discharge. Also under consideration is developing criteria for smaller animal feeding operations.

Have a question?

Not completely sure how to proceed with your project to be compliant with permitting? At SEH, our specialists are ready to provide any guidance you need to make sure your project stays on track.

We have worked with farmers and CAFOs across Wisconsin to design and implement system improvements. We help owners navigate the permit approval and construction documents. Beyond the permitting, we manage the construction staking, inspections, and the development of systems to manage waste. We are supported by a team of SEH engineers, architects, planners and scientists who’ve been doing this type of work for several decades.

Dan Hedrington
Client Service Manager

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