Iowa’s largest water utility is threatening to sue three rural counties for allowing excess farm chemicals to contaminate drinking water, a dispute that is triggering a wider debate over the best way for Midwestern states to stop pollution from fertilizer runoff.

The Des Moines Water Works’ action is being closely followed by environmental advocates and could have far-reaching implications for states like Minnesota that have battled similar threats to drinking water.

Leaders in Iowa’s $30 billion agricultural industry, many of whom rely on nitrogen to fertilize crops, are railing against the move and say the problem requires cooperation with farmers, not more regulation. Gov. Terry Branstad has even accused Des Moines of declaring war on rural Iowa.

But officials at the Des Moines utility, which spends as much as $7,000 a day on a special treatment to remove nitrates from drinking water, say they’re just doing their job.

“In this state, obviously, industrial agriculture is king,” said Bill Stowe, CEO and general manager of the utility. “We’ll continue to get a lot of blowback, but our ratepayers are first and foremost in our minds and they’re tired of paying for other people’s pollution.”

Minnesota, too, struggles with high nitrate levels in rivers and groundwater, mainly in southern counties, but regulators here have favored a collaborative approach with farmers over legal action.

Four years ago, Deborah Swackhamer, a University of Minnesota water quality researcher, presented the Legislature with a 25-year plan to clean up the state’s waters and recommended stricter pollution limits for farmers. She noted last week that nitrate levels in Minnesota waters are still rising.

“[There’s] a lot of concern [about] how long would it take for the voluntary approaches to actually show a difference,” she said. “And do we have time to do that? Iowa has said, ‘No, we don’t have time.’ ”

Who regulates farmers?

Des Moines Water Works wants to sue the three counties under the federal Clean Water Act. It claims that the 10 drainage districts they oversee in northwest Iowa should do more to stop the discharge of pollutants into the Raccoon and Des Moines rivers, key sources of drinking water downstream. The utility wants them to obtain federal permits that would limit the nitrates that go into the system.