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Agriculture is the largest contributor to water pollution in the U.S., dumping millions of pounds of nitrogen and phosphorous into the nation’s waterways each year.

But as the problem worsens and government scrambles to find a solution, a program offering regulatory exemptions to farmers who voluntarily take cleanup steps is getting terrible reviews.

In March 2011, a high-ranking EPA administrator circulated an internal memo to the agency’s 10 division chiefs with a startling assessment: over the past 50 years, levels of nitrogen and phosphorus in the nation’s water supply had “escalated dramatically” and could become “one of the costliest and most challenging environmental problems we face.”

Excess nitrogen and phosphorous in water can kill fish, damage ecosystems, and cause infant illnesses, and in the past 10 years, violations of nitrate pollution in drinking water have doubled.

The EPA has long been at a disadvantage in combating agricultural pollution. In 1977, Congress passed an amendment to the Clean Water Act that exempted many forms of agricultural pollution, making it difficult for the federal government to regulate the industry.

By 2011, the severity of the pollution problem warranted new innovations. The EPA and the U.S. Department of Agriculture settled on an approach called “agricultural certainty,” giving farmers incentives to voluntarily make their properties more environmentally friendly by promising them as many as 10 years of immunity from further regulatory requirements.

Touted by USDA Secretary Tom Vilsack as a strategy that would ensure “farmers will know the rules of the game while the state, EPA, and the public will know that this program will lead to cleaner water,” the approach has spread to states across the country, with the support of millions of dollars in federal funds.

“Investing resources in [agricultural] certainty programs is a wise and strategic investment in conservation,” said Justin Fritscher, a spokesperson for the USDA’s Natural Resources Conservation Service (NRCS).

Yet agricultural certainty is largely untested, seemingly unpopular in the earliest states adopting it, and destined to fail, according to at least one expert on voluntary environmental programs.

In January 2012, USDA secretary Tom Vilsack, then-EPA administrator Lisa Jackson, and Minnesota Governor Mark Dayton participated in the public signing of an agreement, establishing the first federal-state agricultural certainty program. Minnesota seemed like a logical early adopter, with 27 percent of the state’s waterways too contaminated for consumption, according to a recent report by Minnesota’s Pollution Control Agency.

The Minnesota program was the first to offer regulatory exemptions in return for voluntary participation. It was modeled on the Sage Grouse Initiative (SGI), a largely successful collaboration between the U.S. Fish and Wildlife Service (FWS) and the USDA’s Natural Resources Conservation Service (NRCS). The initiative’s goal was to restore the Sage Grouse, a bulky, ground-dwelling bird once common on prairie land throughout the American West, whose population had dwindled due to ranching and natural-gas development.

It all started in 2002 when the U.S. Fish and Wildlife Service received a petition to list the Sage Grouse under the Endangered Species Act. The federal government instead proposed an alternative that, if successful, would help the Sage Grouse rebound without drastic regulatory action feared by ranchers.

Landowners would work with NRCS to voluntarily set aside habitat in “core areas” where Sage Grouse were plentiful, with the goal of restoring the species to 75 percent of its former abundance. If that didn’t happen, the Sage Grouse would be listed as endangered, sparking a robust government intervention. However, the ranchers who participated in SGI would be exempt from further penalties. Early signs suggest the program is working.

So when confronted with the need to draw up a program to incentivize farmers to reduce pollution, NRCS looked to the Sage Grouse Initiative as a road map. In 2011, then-NRCS chief Dave White presented SGI as a model for what Minnesota could achieve with agricultural certainty. In Maryland, when NRCS and EPA officials met with state Department of Agriculture staff, they discussed SGI and what it had accomplished.

There’s just one problem, according to an independent expert on the Sage Grouse Initiative and agricultural certainty: the two approaches are not similar at all, and comparing them is misleading.

“With agricultural certainty, we are dependent on random acts of conservation,” said Sherry Enzler, a research fellow at the University of Minnesota’s Institute on the Environment, specializing in incentive structures for voluntary environmental programs.

In the Sage Grouse Initiative, ranchers who refused to participate were setting themselves up to face severe penalties under the Endangered Species Act, providing a strong inducement to get on board, said Enzler.

Unlike the Sage Grouse program, which created a specific conservation goal of restoring the species to 75 percent of its historic population, the “Certainty Framework” released by USDA and EPA in 2011 mentioned no specific water quality goals, and did not advise targeting areas where conservation practices would lead to greater pollution reductions.

As the federal government has continued to promote certainty programs across the country in states like Virginia and Vermont, skepticism about the approach in Minnesota and Maryland is on the rise.

Brad Redlin, who coordinates the certainty program for the Minnesota Department of Agriculture, voiced doubts in a recent interview with the Spectator that the initiative will result in water quality improvements because the state has no control over whether farmers will sign up.

“We’ll get more bang for the buck if we get the right places and the right producers certified,” Redlin said. “But agriculture is a voluntary participant in clean water. We can’t force anyone to participate.”

At this point, the Minnesota Farm Bureau, the largest organization representing farmers in the state, has not formally endorsed agricultural certainty and has designed its own competing program, the Green Star Farms Initiative, a “farmer developed, farmer driven environmental assessment tool.”

“Even though [agricultural certainty] has been around for longer than a year, most farmers would tell you that they have more questions than answers,” said Kevin Paap, a fourth generation corn and soybean farmer and Farm Bureau representative from southern Minnesota. “We still don’t know what we are getting from certainty and how we are going to be measured.”

The Minnesota program has six million dollars in funding, including three million from NRCS, and three million from the Minnesota legislature.

In Maryland, despite a bruising legislative battle to approve an agricultural certainty program and much fanfare surrounding the May signing of the bill by Governor Martin O’Malley, farmers who sit on an advisory committee are unconvinced that it will attract many participants.

“Certainty is not well received right now. From my perspective this is dead in the water,” Paul Spies, a grain producer and agriculture advisor at the Chester River Association, said at the June meeting of the advisory committee.

Likewise, Maryland Agriculture Secretary Buddy Hance told the Spectator in an interview that the state was not expecting many takers.

“We don’t believe there will be a large sector of farmers signing to the certainty program. It’s a stringent program,” Hance said. “Most of them will believe there is not a significant benefit for them to participate.”

Maryland plans to implement agricultural certainty using a $600,000 grant from the USDA.

Meanwhile, environmental advocates are concerned that time and resources spent pushing agricultural certainty in Maryland are causing better projects to be ignored.

“I feel very concerned about the program,” said Josh Tulkin, director of the Maryland Sierra Club. “There are a lot of unanswered questions, and a lot more promising programs that Maryland could be focusing on.”

Alison Fairbrother is the director of the Public Trust Project, a nonpartisan, nonprofit organization that investigates the manipulation of scientific research by corporations and government. Follow her @adfairbrother