Mike Werling shoulders his way into a field of head-high corn and peers down a row.

“That’s a beautiful sight!” he exclaims.

It was not the corn that delighted Mr. Werling in late September as much as what was growing underneath. Shoots of rapeseed and rye poked up through the dirt, spreading a green flush beneath the tangled leaves. The new plants, sown the week before into the ripe corn, will remain in the field long after the harvest. They’ll protect the soil over the winter and absorb nutrients that might otherwise find their way into the St. Marys River, whose brown-green waters flow past Werling’s farm on their way to Lake Erie.

Werling is a determined and enthusiastic conservationist. A corn, soybean, and grain farmer in northeastern Indiana, he has tried almost every trick in the book to stop erosion and loss of nutrients from his fields that pollute the river – a problem that has produced giant algal blooms in Lake Erie and turned its water to pea soup. In 2014, Toledo, Ohio, had to shut down its water supply.

“I’m ... trying to figure out how I can do better,” Werling says. “There’s always room for improvement.”

More than four decades after passage of the Clean Water Act, which cut effluent from industries and sewage treatment plants, agriculture has emerged as the biggest threat to water quality in many parts of the United States. Phosphorus and nitrogen from manure and synthetic fertilizers are causing problems not only in the Midwest, but also in places like the Gulf of Mexico, where a “dead zone” has formed as big as Connecticut.

Still, there are signs of change. Farmers are becoming more aware of nutrient pollution and agriculture’s contribution to it, says Wayne Fredericks, a corn and soybean farmer in Iowa and president of the Iowa Soybean Association. And a growing number of them, including both Werling and Mr. Fredericks, are adopting practices known to curb, if not eliminate, nutrient pollution. Many worry that if they don’t do more on their own, government will force them.

“We know we have issues here,” Fredericks says.

The soybean association promotes new conservation strategies, such as building artificial wetlands and underground “bioreactors” to capture nutrients in drainage systems. A research program encourages members to experiment on their farms and share the results with others. Fredericks, for one, has been trying different kinds of cover crops, including radishes, sometimes scattering the seed from airplanes.

Werling also has tried plenty of things. He has stopped plowing, planted swaths of grass to slow runoff and filter out sediments, engineered a drainage ditch to become a long wetland in heavy rain, and figured out how to inject fertilizer into the ground when he plants instead of scattering it on the surface beforehand.

But many farmers remain skeptical. “They ask me why I’m wasting my money on cover crops,” Fredericks says. Most farmers are reluctant to depart from established methods, he says. They are especially reluctant to do anything that could increase their costs or reduce their yields.

Economics of curbing the problem

Indeed, the economics of curbing nutrient pollution has been a major obstacle. Conservation on farms has long depended on the voluntary participation of individual farmers, with federal and state governments, and sometimes private groups, offering financial incentives. The subsidies help because while farmers bear most of the costs of curbing the pollution, most of the benefits accrue downstream.

And the costs are high. For example, the US Department of Agriculture’s Mississippi River Basin Healthy Watersheds Initiative is spending $30 million a year to reduce nutrient pollution in dozens of high-priority watersheds. Fertilizers washing down the Mississippi each summer create the dead zone in the Gulf. However, it would cost $2.7 billion annually to reduce nutrient pollution enough to shrink the area, a 2014 study estimates.

This dilemma has inspired some agricultural scientists to seek more cost-effective solutions. In Wisconsin, the Pecatonica River Project grew out of controversy over a proposal to require all Wisconsin farmers to install buffer strips – swaths of grass – along rivers and streams to reduce phosphorus pollution. The project targeted the worst polluters instead. After subsidizing improvements on eight farms, researchers found a 37 percent decrease in phosphorus in the Pecatonica.

“What we wanted was to find something that works within a given system to produce a reduction of phosphorus, but also works for the producers,” says Laura Good, a soil scientist at the University of Wisconsin-Madison.

Market-based approaches

In some places, farmers, industries, and municipalities are trying market-based approaches, including water quality trading. Such trading allows industries and municipalities to meet their pollution-control obligations by paying local farmers to adopt conservation practices.

One of the oldest projects involves Amish farmers and the Alpine Cheese Co. in Winesburg, Ohio. When Alpine wanted to expand a decade ago, it faced the prospect of spending millions of dollars on new wastewater treatment equipment. Instead, Alpine agreed to pay local farmers, some of whom sold milk to the company, for conservation efforts that resulted in twice the pollution reduction than the technology alone could have achieved.

“It’s just a huge success story,” says Richard Moore, an environmental scientist at Ohio State University and a proponent of small-scale, community-based trading. “Everyone looks at it and sees win-win.”

The Ohio fertilizer industry is trying another market-based approach, with help from the Nature Conservancy: a voluntary certification program for businesses that sell and apply fertilizer on farms. The program trains workers to use scientific principles when deciding the amount, timing, and method of application. For example, it’s better to fertilize close to planting time than in the fall after the harvest.

The program also requires soil testing to determine just how much fertilizer a field really needs. Farmers often apply too much, researchers say.

Dubious of the results

While supporters extol these and other efforts, many experts are dubious. They say that current efforts, however promising, are just too little to make a meaningful difference, and they question the voluntary approach long favored by federal and state governments and most farm groups.

“The fundamental problem is we’ve relied almost entirely on voluntary programs – in a sense bribing farmers to do this, putting money on the table and hoping to attract volunteers,” says Craig Cox, senior vice president for agriculture and natural resources at the Washington-based Environmental Working Group. “That approach has failed, for a whole bunch of reasons.”

The Clean Water Act doesn’t allow the federal government to regulate agriculture, but it does give the government authority to set water quality standards. In some places, like Chesapeake Bay, the Environmental Protection Agency has used this authority to force states to set limits on nitrogen and phosphorus and to develop strategies for meeting the limits. But critics say it has been reluctant to push too hard.

“The states are not very happy with notions of a strong federal presence,” says David Moreau, a research scientist at the University of North Carolina in Chapel Hill. A 2012 National Academy of Sciences report that Professor Moreau oversaw concluded that reducing nutrient pollution in the Mississippi River basin needed stronger federal leadership – which he says has not come.

In a few cases, regulatory pressure is mounting at the state level. Worried about conditions in Lake Erie, the Ohio legislature last year passed a law forbidding farmers to apply manure and other fertilizers on frozen ground and before heavy rains.

Meanwhile, environmental groups and others are applying legal pressure to try to force governments – and farmers – to do more. One place is Iowa. In March, the Des Moines Water Works sued the supervisors of three rural counties over agricultural drainage that officials say is responsible for rising levels of nitrates in the Raccoon River, a source of the city’s drinking water. The case, which could also have consequences for farmers in other areas, is scheduled to go to trial next year.

Good news, bad news

“These are not simple questions,” says Bob Perciasepe, a former EPA official who heads the Center for Climate and Energy Solutions, a nonprofit in Arlington, Va. “But the good news is we generally know what needs to get done. The bad news is we’ve yet to figure out what the approach is to make that happen.”

On his farm in Indiana, Werling says he doesn’t have all the answers. But he keeps tinkering, trying new things. For him, as for many farmers, conservation is as much art as science, as much skill and conviction as biology and economics.

“It’s a matter of learning a new way of farming,” he says.

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Occasionally, Werling invites other farmers to see what he’s been doing. A hundred or more will show up on these days. Not many are prepared to follow his example.

“I’m unusual in the way I farm,” he says. “But I think it’s the right way to solve the problem.”