Cows at a Dunn County dairy farm. (Photo by Henry Redman/Wisconsin Examiner)

A Wisconsin Court of Appeals on Wednesday ruled that the state Department of Natural Resources has the authority to require that factory farms obtain water pollution permits, affirming a previous Calumet County court decision. 

Two groups representing Wisconsin’s factory farms, known as Concentrated Animal Feeding Operations, filed the lawsuit in 2023, arguing that the state did not have the authority to require permits under the DNR’s Wisconsin Pollutant Discharge Elimination System (WPDES) program. The program requires any entity that discharges pollution into the state’s waterways to obtain a permit. 

The lobbying groups, Venture Dairy Cooperative and the Wisconsin Dairy Alliance, are themselves led by factory farm operators who have been cited by the DNR for contaminating the state’s water through manure spills. Wisconsin Manufacturers and Commerce, the state’s largest business lobby, has also been involved in the lawsuit. 

State law requires an application for a WPDES permit must be made within 90 days of becoming a factory farm or expanding. The permits last for five years before they must be renewed. CAFOs — factory farms with more than 1,000 “animal units,” which is equivalent to about 700 milking cows — are also required to submit plans to the DNR for how they intend to manage the manure created on the farm. 

Over the last two decades, the number of CAFOs operating in Wisconsin has more than doubled, creating an increasing amount of manure that sits in lagoons, gets spread onto fields and potentially runs off into local waterways. 

If a manure spill occurs, the permit requires the owner to notify the agency and is responsible for the cleanup. The permits also need to be reapproved whenever an operation is planning to expand and every permit application is subject to a public comment period. 

A manure spill can cause harmful substances such as nitrates, E. coli and phosphorus to enter the state’s ground and surface waters — potentially making drinking water dangerous to consume and causing fish to die. 

Four years ago, the Wisconsin Supreme Court ruled that the DNR had the authority to use the WPDES permits to impose conditions on factory farms as a way to control their environmental effects. In recent years, WMC has filed several lawsuits seeking to weaken the DNR’s authority and undermine its ability to regulate water pollution across the state. 

The lawsuit argued that having to comply with the “time-consuming, costly process” of obtaining a permit that imposes “substantial costs and regulatory burdens” on the farms, is against the law because of two previous federal court decisions in 2005 and 2011 about the U.S. Environmental Protection Agency’s own permit requirements for polluters.

On Wednesday, the District II Court of Appeals, which covers 12 counties in southeastern Wisconsin, found that the DNR does have the authority to create the rules the dairy groups challenged. 

“The challenged rules do not exceed the DNR’s statutory authority and do not conflict with state law,” the three judge panel, controlled by a conservative majority, wrote.

After the decision, advocates for the environment and smaller farms said it would help the state protect water quality. 

“This decision is a win for every rural community that depends on clean water,” Wisconsin Farmers Union President Darin Von Ruden said in a statement. “Family farmers understand that stewardship of the land and water is key to long-term success. Ensuring that large livestock operations follow commonsense permitting rules protects our shared resources and the future of farming in Wisconsin.”

“These large operations can produce as much waste as a small city, and the state must be able to monitor and control how, where, and in what quantities manure is stored and spread on the landscape,” said Clean Wisconsin attorney Evan Feinauer. “That’s why for nearly 40 years, the DNR has required large CAFOs to have permits to limit this dangerous pollution. Allowing large dairies to sidestep oversight would have been catastrophic for water protection in our state.”