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.”

The stormwater pond at the Emerald Sky Dairy in St. Croix County that was polluted after a 2016 manure spill. A new survey finds that waste produced in the St. Croix River watershed is as much as if more than 3 million people lived there. (Wisconsin DNR photo)

The waste produced by livestock in the St. Croix River watershed is equivalent to 3.25 million more people living in the region, according to a study conducted by a retired University of Iowa professor on behalf of local clean water activists. 

The study, conducted by Dr. Chris Jones, who studied water quality and agriculture at Iowa, totals the number of beef cattle, dairy cows, hogs, chickens and turkeys across the river’s watershed in Minnesota and Wisconsin, calculates the amount of waste those animals excrete in terms of nitrogen, phosphorus and solids. It also  projects  how many  humans it would take to produce that much waste. 

“Some of these nutrients from the manure get into our streams, we know that,” says Jones, who has authored a book about the effect of factory hog farming on the water in his home state. “And so, since the waste is not treated, and since the distribution of it on the fields is not very regulated … this volume of waste certainly makes the river and its tributaries more vulnerable to nutrient groups.”

In recent years, western Wisconsin has become the site of the state’s most intense fights over factory farming. Most of the state’s largest farms, known as concentrated animal feeding operations (CAFOs), have been in the eastern part of the state. But large agricultural companies have been working to expand factory farming operations across western Wisconsin’s Driftless Region and the St. Croix watershed. 

That effort to expand has sparked a growth in local opposition. A number of communities have worked to pass local ordinances regulating how and when a factory farm can be built or expanded within their borders. Industry groups have filed lawsuits to block those efforts. 

Community members have also worked to stop or change permitting decisions by the state Department of Natural Resources for the expansion of factory farms. 

“I think it’s very important for citizens to realize that the counties and other local governments retain some power in being able to zone their land for the construction of these CAFOs because, as I said in Iowa, when the counties lost control, that’s when the big expansion occurred,” Jones says.

Despite local opposition, CAFOs have continued to grow, causing increased amounts of nutrients in the local water systems. Runoff and manure spills have caused massive fish kills in local streams, beaches have regularly been closed due to excessively high levels of pollutants and the groundwater — the sources of drinking water for most rural residents — has been found to contain high levels of nitrates. 

The St. Croix River has been part of the National Park System as a Wild and Scenic River since 1968 and listed as an “impaired water” by the Environmental Protection Agency since 2012. 

According to Jones’ study, most of the livestock within the watershed is raised on the Wisconsin side of the border. The waste created by just the livestock in Barron County is equivalent to 1.7 million extra people. The livestock waste in St. Croix County is equivalent to 911,000 more people.

The population of Barron County is about 46,000 and of St. Croix County is about 96,000, according to U.S. Census data. 

Jones says it’s within the capabilities of the regulating agencies and university systems in both Minnesota and Wisconsin to calculate the exact number of livestock the watershed is capable of enduring. He says they should do that, because the industry won’t. 

“This is an approach the state should think about in regulating these areas on a watershed by watershed basis, based on what we assume they can endure,” he says. “And that ought to be done for the Saint Croix to protect it.”

He doesn’t expect the St. Croix River’s designation as a national waterway by itself to influence the agriculture industry to change its practices.

“We have evidence here in Iowa, but any special status that the streams have is not going to affect decision making on the ag side, it’s just not,” Jones says. “So the state’s got to try to get in front of this and get their arms around it, because once the horse leaves a barn, it’s too late.”