Minnesota Asks the Public Whether Groundwater Rule Is Enough to Curb Farm Fertilizer Pollution, Following Lawsuit

Minnesota regulators are asking the public whether the state’s rule to prevent agricultural nitrate pollution is strong enough to protect drinking water.

Nitrate levels rose in almost two-thirds of Minnesota community water systems tested between 1994 and 2018, according to an Environmental Working Group analysis. In southeast Minnesota alone, state data show that nearly four out of every five people are affected by high nitrate concentrations, in addition to thousands more who rely on private wells, which are not monitored by the state.

More than 70% of the nitrates entering Minnesota waters are from cropland, with the remaining sources including wastewater treatment plants, septic systems and urban runoff. Nitrate pollution in drinking water is linked to increased cancer risk in adults and acute, life-threatening illnesses for children, including methemoglobinemia, or blue baby syndrome.

Following a lawsuit, the Minnesota Department of Agriculture is accepting comments through March 12 on its Groundwater Protection Rule, a policy intended to limit nitrate contamination from farm fertilizers.

The three environmental groups that filed the lawsuit say that the existing policy has failed to curb contamination in the state’s drinking water, while some agricultural researchers argue the problem is more complex than regulating fertilizer use.

Protecting Minnesota’s Most Vulnerable Areas

The Groundwater Protection Rule only addresses part of the nitrogen entering Minnesota’s soils. The rule applies to commercial fertilizer use, which accounts for an estimated 75% of the nitrogen that is applied to agricultural fields in Minnesota. The remaining 25% of nitrogen applied to fields is from animal manure, which falls under the Minnesota Pollution Control Agency.

The January 2025 litigation, filed by the Minnesota Center for Environmental Advocacy, Minnesota Trout Unlimited and the Minnesota Well Owners Organization, alleges that the state Department of Agriculture and the Minnesota Pollution Control Agency did not sufficiently protect the state’s most vulnerable areas from nitrate pollution. In September 2025, a district court ordered the state Department of Agriculture to investigate whether additional restrictions are needed.

The state agency adopted the Groundwater Protection Rule in 2019 to minimize nitrate contamination in the state’s most vulnerable areas, or those where nitrate can easily move through soil and into groundwater: six counties in north-central Minnesota known as the Central Sands region, and the southeastern corner of the state, which is characterized by a very porous underlying geology. The rule restricts commercial fertilizer application in these areas in the fall and on frozen soil, practices known to lead to significant leaching and runoff into water sources.

But critics argue that this restriction is unlikely to have an impact. Even before the 2019 rule went into effect, only 6% of corn producers in sandy soils and 12% in the southeastern region — the areas targeted by the rule — applied commercial fertilizer the previous fall, according to a survey of more than 50,000 respondents by the state agriculture department. The agency itself notes that the vast majority of Minnesota farmers do not apply fertilizer in the fall or to frozen ground.

“It’s very cheap to tell people to not do something that they’re not already doing,” says Joy Anderson, a supervising attorney at the Minnesota Center for Environmental Advocacy. “You made a change, but it doesn’t actually make producers mad at you.”

Critics also say the rule’s implementation timeline has slowed meaningful action. It includes built-in, staged delays that prioritize voluntary actions over regulations.

“It’s been six years since the groundwater protection rule was put into place, and we’re not seeing any improvement,” says Anderson.

Tackling Animal Manure

Regarding animal manure applied to fields, which also contains nitrogen, Minnesota’s rules governing animal feedlots were last updated in 2000. But the state’s manure production has become more concentrated in the past few decades: The number of large concentrated animal feeding operations in Minnesota has tripled since 1991. The Pollution Control Agency held a public comment period in 2025 to kick off its revision process. Draft changes, including recommended manure application practices to address nitrates, are expected after 2027, according to the agency’s website.

“Manure is particularly problematic, even though it’s a smaller amount of the nitrogen that’s applied, because surveys show that producers apply more nitrogen to fields when they combine manure and commercial fertilizer,” says Anderson.

It is unclear how much nitrogen is in manure compared to commercial fertilizer, Anderson says, so farmers will often apply extra. Manure is also often applied during periods when crops cannot absorb nutrients, such as the fall season after harvest, increasing the likelihood of nutrient runoff or leaching.

“You have to address it holistically. You have to address both commercial fertilizer and manure,” says Anderson.

Currently, Minnesota feedlots with more than 1,000 animal units are required to implement best management practices intended to reduce nitrate pollution when applying manure in the fall. Feedlots with more than 300 animal units must maintain a manure application record-keeping form, but they are not required to submit it to the state.

Brad Carlson, water resources extension educator at the University of Minnesota Extension in Mankato, says that because only larger feedlots’ manure applications are tracked — and commercial fertilizer application is not tracked at all — it’s difficult to know the total amount of nitrogen farmers are applying to fields across the state.

“It’s the smaller operations typically that are lacking storage, they’re lacking technology to do more timely applications and so forth,” says Carlson. “A lot of the smaller operations… No one’s really paying attention to what they’re up to.”

Carlson also argues that changes in fertilizer practices since the 2019 Groundwater Protection Rule would not yet be reflected in groundwater quality tests. It takes decades for water infiltrating the ground at the surface to fully reach the groundwater in Minnesota, according to a 2025 study by the state department of agriculture and the University of Minnesota. The study found that Minnesota groundwater in shallow springs and wells ranged from 10–40 years old, while the groundwater in deeper aquifers could be thousands of years old.

This means that even if nitrates have been reduced for the seven years following the rule change, that may not show up in the groundwater for a few more years or even decades, depending on the region. “If the water we’re testing as high in nitrates was actually up on the top 30 years ago, it’s pretty unrealistic to think that any changes we made in the last five years have made any difference,” says Carlson. But that doesn’t automatically mean that the current approach is working, either, he says.

A 2020 Environmental Working Group analysis estimated that — based on manure production and commercial fertilizer sales numbers — 96% of Minnesota’s agricultural counties exceeded nitrogen fertilizer recommendations. In 13 counties, nitrogen applications were estimated to surpass recommendations by more than half.

Carlson says producers should follow recommended fertilizer best practices and adopt strategies like cover cropping and incorporating perennials into the landscape: “There’s a host of practices that can be effective in reducing nitrates in water.”

Who Bears the Cost?

States vary widely in their approach to nitrate management, and many lack robust enforcement. However, some states are now proposing legislation to reevaluate manure management and monitoring.

Iowa, where concentrated feeding operations produce 110 billion pounds of manure per year, does not collect data on where and how much manure is spread. But last month, state lawmakers proposed a package of bills aimed at reducing nitrate pollution in waterways, including requiring water pollution monitoring at more than 4,000 large livestock facilities. And in California, the recently introduced Assembly Bill 2100 would require the state’s Department of Food and Agriculture to create a process for approving new manure-management projects that involve either selling or transferring manure offsite, or on-farm composting.

For Anderson, nitrate pollution is a systemic problem. Better distributing the costs could help shift the broader system that drives nitrogen use.

“The fact is, when you are a producer and you apply too much nitrogen, you might see a benefit from that, you might not…[but] you have almost no additional costs,” says Anderson. “The costs are imposed on people whose private wells are contaminated, who will have medical issues because we are drinking contaminated water, on cities that have to dig new wells or implement really expensive treatment processes for nitrates.”