The Minnesota Pollution Control Agency finalized the changes to two of its general permits for feedlots this month, which typically apply to those with 1,000 or more animal units. The changes, which go into effect June 2025 and February 2026, have some farmers worried, but others relieved.
The main changes are an online tool to develop a manure management plan, added regulations for tracking data when transferring manure to someone else and some prohibitions on manure applications to ensure best management practices.
Many of these changes are “steps in the right direction,” said Matthew Sheets, a policy organizer with the Land Stewardship Project, a nonprofit with a focus on sustainable agriculture.
Prior to the plan being finalized, people with various ties to the permitting system voiced their likes and dislikes during an open comment period.
Sheets said he’s happy with the requirements for tracking manure application.
“For a while it has been that the way that large CAFOs (Concentrated Animal Feeding Operations) are able to get rid of some of their liquid manure is by working with somebody else who is going to apply that on their fields. They essentially sell it to another person. And up until now, at that point of sale, that’s where the tracking stops as well,” Sheets said. “In these new rules, the tracking doesn’t stop there.”
He wants more tracking about groundwater quality, but including this manure specification is a good step, he said.
Hesitations about tracking
Others, like Loren Dauer, the public policy director at the Minnesota Farm Bureau Federation have concerns about application tracking and its associated information. While he’s happy to see the tool online and on an accessible platform, he’s concerned that the owner of the feedlot that’s producing the manure will have the responsibility of collecting that data and sharing it with the state.
“If you’re the farmer or the landowner who utilizes manure, you are now going to be required to essentially give up your crop history data,” he said. “From our perspective, this was proprietary data. These are farmers, individuals that utilize this information, and if you’re a larger feedlot, and you’re providing this manure to several other landowners or farmers … does that one feedlot have the right to hold all that information and report that back to MPCA? In our opinion, that should not be the case, because it is kind of private.”
He suggested the MPCA instead collect the information separately instead from the permittee (who’s providing the manure) and the receiver of the manure.
Glen Groth, the president of the Winona County Farm Bureau Federation, said he’s heard concerns about how this will be tracked.
“If you give manure to a neighbor or sell manure to a neighbor, you’re expected to ensure they comply with the current manure application regulations. Well, how do you make them comply to it? And then, you know what happens if they say, ‘Yeah, you bet I’ll put down the cover crop within a certain amount of time,’ and then they don’t? … How do you hold your neighbor to account?”
The MPCA has stated that feedlot owners are required to ensure manure application is done appropriately and, if a manure recipient consistently fails to comply, then the permittee should consider no longer doing business with that recipient. If despite the permittee’s best efforts, recipients don’t follow the regulations, MPCA can take enforcement action against the manure recipients.
Those at the Land Stewardship Project disagree, saying that the requirement isn’t necessarily onerous.
“Even though that is something that is an additional piece that must be kept by the person that is spreading that manure and the operator of the CAFO … it is just one of the bare minimum things that we can be doing to support and ensure that our the best management practices are going to be adhered to,” Sheets said.
Groth and Dauer are also concerned about the best management practices that are required for permit holders, which include specific practices such as applying the manure to a growing perennial or row crop or planting cover crops to a range of other practices depending on the time of year. There are specific regulations for the areas that are considered “vulnerable groundwater areas.”
The MPCA has stated it will recognize “good faith efforts” to establish a cover crop because of weather uncertainty, which can impact cover crop growth.

But the Minnesota Farm Bureau Federation feels these regulations, when coupled with the existing Groundwater Protection rules, may have farmers in a bind.
“With the Groundwater Protection rule from the Department of Agriculture, you’re not allowed to apply commercial fertilizer during the fall time without some of these practices. And so a lot of these farmers have kind of turned to using manure from livestock to kind of fill their needs and their nutrient plans,” Dauer said. “We’re not providing a lot of options for our farmers to have nutrient plans in these areas because this new groundwater vulnerable area, is also similarly where the Groundwater Protection area is as well.”
Groth, who’s not too worried about the impact of these regulations on his own crop operation, said he’s heard from farmers in his area about how these new rules could affect them.
He’s worried that these new rules may potentially inform future regulations on feedlots, especially expanding these regulations to those who don’t currently need to apply for the permits because of the size of their feedlots.
“If these regulations apply to smaller family farms, they could be very difficult and very expensive to comply with,” Groth said.
He said it’ll be financially challenging for farmers to do some of those best management practices, especially regarding manure application, if it has to be done in the spring.
“The rule says that manure can’t be applied in the fall unless certain conditions are met, or it has to be applied in the spring. Manure applied in the spring, that could greatly increase the amount of manure storage someone has to have, which is very expensive on farms these days. And it could be just a time constraint. We have situations where it’s gone from snowy and frozen to perfect planting field conditions in two weeks. Two weeks aren’t enough for a lot of farmers to get their manure applied in a responsible manner, or to even hire somebody to do something like that.”
Future impacts on feedlots
In Winona County, Groth estimated there are just a handful or two of feedlots that apply for these permits. But there are many farms on the edge, meaning having just a couple more cows would require them to apply for this permit.
“There’s a lot of farmers, far more than just a handful, that are just right on that cusp of needing this or not. So the concern is, if this is baked in the law, these somewhat impractical new requirements, that they could lower the threshold at some point in the state of Minnesota … meaning (farms) somewhat suddenly would have to comply with these rules,” Groth said. “And then (that would) apply to hundreds of farms in the county rather than just five to 10 or a couple dozen.”
He worries that these regulations would prevent farms that want to expand from doing so.
“I think you see a bit of that in Winona County already. We got this extremely low animal unit cap. And I think you see a number of people in Winona County farm families that either they get away with it by having to own two or three facilities rather than one, which is not efficient from an environmental permitting and manure management standpoint, nor is it from a purely economic production standpoint,” he said.
Groth said a solution is needed that would reinvigorate the dairy industry. He thinks being more liberal with permitting dairy facilities to encourage more dairies could be one of the ways to achieve better groundwater quality, and encouraging perennial crop production like alfalfa, which is feed for cows and also helps reduce nitrate contamination in groundwater.

Ava Kian
Ava Kian is MinnPost’s Greater Minnesota reporter. Follow her on Twitter @kian_ava or email her at akian@minnpost.com.