MANSON, Iowa — The flat, endless acres of black dirt here in northern Iowa will soon be filled with corn and soybean seeds. But as farmers tuned up their tractors and waited for the perfect moment to plant, another topic weighed on their minds: a lawsuit filed in federal court by the state’s largest water utility.

After years of mounting frustration, the utility, Des Moines Water Works, sued the leaders of three rural Iowa counties last month. Too little has been done, the lawsuit says, to prevent nitrates from flowing out of farm fields into the Raccoon River and, eventually, into the drinking water supply for roughly 500,000 Iowans. The suit seeks to make farmers comply with federal clean-water standards for nitrates that apply to factories and commercial users, and requests unspecified damages.

“It’s very clear to me that traditional, industrial agriculture has no real interest in taking the steps that are necessary to radically change their operations in a way that will protect our drinking water,” said Bill Stowe, the chief executive of Des Moines Water Works. High nitrate runoff, which can result from nitrogen-rich soil and applied fertilizer, places Des Moines’s drinking water in danger of violating federal quality standards, Mr. Stowe said, and increases costs and poses health risks for customers.

The lawsuit raises not only the legal question of whether the government should regulate the water that drains off farmers’ land, but also the existential issue of whether rural and urban Iowans can collaborate to solve vexing problems. In a state where agriculture drives the economy, grain silos are featured on license plates and people pride themselves on a certain brand of “Iowa nice,” farmers like Brent Johnson have criticized the litigation as an antagonistic overreach that comes at the expense of cooperation and neighborliness.