EGLE Director Issues Decision in CAFO General Permit Dispute

A recent Opinion released by Phillip D. Roos, the Director of the Michigan Department of Environment, Great Lakes, and Energy (EGLE), decided a key issue in the ongoing legal battle regarding the Concentrated Animal Feeding Operations (CAFO) General Permit.

Since 2020, groups like the Michigan Farm Bureau, the Michigan Milk Producers Association, and the Michigan Pork Producers Association (referred to as the Agricultural Defendants) have been contesting General Permit No. MIG010000, which is a National Pollutant Discharge Elimination System (NPDES) permit that governs the majority of CAFOs in Michigan.

After a Michigan Supreme Court opinion on July 31, 2024, an Administrative Law Judge conducted a contested case hearing and issued a Final Decision and Order (FDO) on January 13, 2025, that largely adopted the Agricultural Defendants’ positions. EGLE and several intervening organizations—such as the Environmental Law & Policy Center, the Michigan Environmental Council, and the Environmentally Concerned Citizens of South Central Michigan—filed petitions for review of the Administrative Law Judge’s decision by the EGLE Director.

On October 29, 2025, Roos released an Opinion that primarily adopted EGLE’s objections to the FDO, thereby reversing in part and adopting in part the FDO. The Director’s Opinion decided the following issues:

Winter land application of manure. The General Permit allowed land application of manure in January, February, and March, though there were some restrictions. The FDO removed land application restrictions in March, so long as the ground was not frozen or covered in snow. Roo’s Opinion reversed the FDO and imposes more stringent restrictions than were contained in the Original General Permit. He held that land application of CAFO waste is entirely prohibited from January 1 through March 19, siding with EGLE’s position that the prohibition is needed to ensure water quality standards (WQS) are achieved and applicable laws are adhered to.

Manifesting CAFO waste during winter months. The FDO removed a prohibition that barred manifesting CAFO waste in March, while retaining the General Permit’s prohibition of it in January and February. To ensure WQS standards are met and there’s compliance with applicable laws and regulations, Roos concluded that manifesting CAFO waste should be prohibited in January, February, and March.  

Total maximum daily loads (TMDL) requirements. In accordance with the federal Clean Water Act, the state must have standards for TMDL for waters with E. coli, dissolved oxygen, biota pollution, and nutrient pollution. Provisions of the Original Permit required that CAFOs conduct a comprehensive evaluation when EGLE determines there are contaminants present in local watersheds, and then submit a comprehensive evaluation to the agency.  

The FDO removed this Permit requirement, deeming it unnecessary to maintain water quality standards. However, the EGLE Director disagreed and imposed more stringent requirements than were contained in the Original General Permit. CAFFOs in TMDL watersheds will be required to abide by individualized requirements in their Certificate of Coverage, which can include conducting comprehensive evaluations to determine if additional pollution control measures must be implemented. The Director held that this requirement was necessary for both WQS standards and to ensure compliance with the Clean Water Act and other applicable regulations. 

Groundwater monitoring requirement. EGLE had requested that a new provision be added to the General Permit requiring groundwater monitoring for CAFO waste storage structures based if specified in a CAFO’s Certificate of Coverage (COCs). The ALJ had determined that he lacked the authority to add new provisions to the General Permit that had not been subject to a public comment and hearing period, but Roos decided that he had the authority to do so.

Notice of application to certain fields. EGLE also wanted a new provision to be added requiring CAFOs to inform the agency that they had applied waste to certain fields specified in the COC within 24 hours. The ALJ had rejected this provision as beyond his authority, but in his Opinion the Director adopted the provision, explaining that this condition is necessary for WQS and compliance purposes. As a result, the Permit has been modified to include this strict reporting provision.

Requirements for manifested CAFO waste. For the intervening environmental groups had requested the addition of a provision that would tighten requirements for manifested CAFO waste, including assessment and corporate ownership disclosure standards for certification. Roos declined the request, stating there was no legal basis to impose these permit requirements.

Phosphorous risk assessment. The draft General Permit required that CAFOs only use the Michigan Phosphorous Risk Assessment (MPRA) to evaluate fields for land application, but EGLE modified it in the issued Original General Permit to also allow Bray P1 levels. The Intervening environmental groups requested that the Permit be reverted to its original language, but the Director denied the request, so the revision allowing field evaluation based on either MPRA or Bray P1 levels remains in place.

Liquid CAFO waste on tile-drained fields. The Agricultural Respondents and Intervenors disagreed on how much solid CAFO waste should be allowed in tiled fields, with the latter arguing that solid content should be less than 8%. Roos denied this request, citing the Agricultural Respondents’ argument that an 8% threshold was based on a faulty premise regarding the flow of liquid manure, and would preclude land application of swine and dairy waste, which typically contains less than 8% solids.

Sampling and testing of tile drain discharges. The General Permit called for inspection of tile drain outlets before and after land application, as well as if there are signs of contamination after rain events that occur within 30 days of application. Environmental Intervenors said this requirement was too ambiguous and requested that analytical sampling be conducted whenever there is a rainfall. This request was denied and the original requirement remains in place.

Storage capacity calculations. The Intervenors and Agricultural Respondents disagreed on what should be considered in storage capacity calculations. The draft Permit stated calculations could not factor in evaporation but could account for 12 inches of residual solids at the bottom of storage structures.

However, when the Original General Permit was released, this requirement was cut in half. The Environmental Intervenors requested that the Permit revert back to the original language, but the Agricultural Respondents opposed this because a 12-inch requirement would skew calculations. Roos agreed with the Agricultural Respondents, keeping the calculation amount at 6 inches.

Daily Manure Application Summary. The Original Permit included a Daily Manure Application Summary requirement, which would compel the reporting of basic waste application facts like time, date, and application method. The FDO removed this requirement, arguing it was inappropriate, and the Environmental Intervenors sought to reinstate it. Director Roos said in his Opinion that the Intervenors did not prove the need for this requirement and ruled against them.

Based on the decisions in the EGLE Director’s Opinion, the daily operations of the state’s agricultural industry may change significantly. If you need guidance on how these changes will affect your business, the attorneys in Foster Swift’s Agri-Business group are here to help.