Tucked away in the massive environmental bill that the Legislature will send to Gov. Mark Dayton in coming days are a couple of tweaks to state irrigation law that could imperil a collection of delicate prairie wetlands known as calcareous fens.

Found in only 10 states, they are specifically protected by Minnesota law because they harbor rare and endangered plants. But after regulators denied irrigation permits to a handful of farmers because of the risk to fens — which altogether occupy a total of 5 square miles of land in Minnesota — Republican lawmakers want to give irrigators priority for often-scarce groundwater.

The two provisions are part of a larger suite of policy changes and funding cuts that, if passed, would strengthen the hand of irrigators at a time when state environmental officials and ecologists are increasingly concerned about overuse of groundwater and rising rates of agricultural contamination in the state’s lakes and rivers.

That’s especially true in the central Minnesota watershed that feeds the Upper Mississippi River and provides drinking water to 1 million people.

“They have profound implications on water sustainability and water management,” said Barbara Naramore, assistant commissioner of the Department of Natural Resources (DNR).

The two provisions on fens provide a window into the competing interests at play.

Farmers and the legislators who support them say state regulators have gone overboard on protecting the rare wetlands while providing insufficient evidence that nearby irrigation pumps would rob them of water.

“They are making their decisions not even based on facts,” said Reed Van Hulzen, a third-generation farmer in Pipestone County who had a long fight with the DNR over an irrigation permit for a well near a small fen. “They are doing it on projections.”

But scientists say the 200 tiny fens across Minnesota are extraordinarily sensitive and ecologically valuable.

Among the rarest of ecosystems globally, they evolved with the prairies over thousands of years and depend on a continuous supply of calcium-rich groundwater that wells up from below.

“Once you lose them, you can’t get them back,” said Megan Benage, an ecologist with the DNR in southwest Minnesota. “These are just as much a part of your heritage as farming.”

DNR officials say water-use conflicts around fens are actually quite uncommon and can usually be resolved. Farmers, sand mining companies and cities have all won DNR approval for permits that include protection plans for fens, officials said.

Still, since 2011 the agency has denied 10 permit requests out of a total of 5,000, and six of them were fen related.

One was Van Hulzen’s.

In 2013 he asked for a permit to irrigate 100 acres of cropland near two calcareous fens. Like many farmers, he’s come to rely on irrigation to increase yields and reduce the risks of drought.

But tests found that at high pumping rates, a small fen in a neighboring pasture showed a slight drop in water levels. Despite protracted negotiations, he was unable to agree with the DNR on a management plan.

“They denied me because of the potential impact,” Van Hulzen said.

Jim Seahl, the DNR hydrologist in the region, said tests clearly showed that irrigation would have drawn down water and harmed the fen.

Appealing the decision would have been too expensive, Van Hulzen said, and he’d likely lose. So instead, he talked to his state senator, Bill Weber, R-Luverne.

Test case

The outcome is language in the Legislature’s omnibus bill that would require the DNR to grant permits that give Pipestone County farmers the right to use groundwater near fens for 15 years.

If after five years the fen is harmed, the DNR could cancel the permit but would have to reimburse the farmer for part of the cost of the irrigation system.

Weber said it’s designed to make Pipestone County a test case for the impacts of irrigation on fens because landowners deserve certainty when their permits are denied.

“To say [fens] need to be protected without the validity of information is, to me, not right,” he said.

A second provision would require the DNR to allow any permit holder in Minnesota to temporarily reduce groundwater levels near fens as part of a protection plan — a step that, ecologists say, could prove fatal for some fens.

Van Hulzen, however, said he doesn’t believe the state needs legal protections for the little wetlands.

After all, he said, no one visits the small fen in the pasture near his fields that triggered all his problems with the DNR, he said.

“Is your life going to change if it goes down?” he asked in an interview. “Is my life going to change?”

Among the other environmental proposals on their way to Dayton’s desk is one that for the first time would allow landowners to sell their state water permits along with the property where the well is located.

It makes sense, supporters say, because the permit is tied to the value of the land. But opponents say it flies in the face of Minnesota’s long history of fair-share water laws.

“Irrigators are pushing Minnesota to adopt [provisions] that assume we are a Western water law state,” said Jean Wagenius, DFL-Minneapolis.

The policy changes are moving alongside a proposed $100 million overall cut in General Fund dollars for the state’s environmental agencies, and a shift of money from the state’s 2008 Legacy Amendment sales tax away from programs designed to manage water conflicts.

GOP leaders say the entire matter is still up for negotiation with Dayton.