In a water cleanup effort more complex than any other in the nation, virtually every community in the 360-square-mile watershed around Madison has agreed to pool resources with farmers to eliminate nutrient-driven weed and algae growths that limit use of lakes and streams.

The agreement signed by about 60 local governments will pool more than $2 million annually for 20 years starting Jan. 1 to pay for measures that keep soil and other material laden with the nutrient phosphorus from being carried into surface water by snow melt and rain.

Unlike previous attempts to eliminate foul-smelling algae blooms and thick tangles of aquatic weeds around Madison, this one does more than pay farmers to make improvements such as planting along ditches and streams to stabilize soil.

It targets land areas known to pollute most and establishes a legally enforceable timetable to reduce phosphorus in water throughout the Yahara River basin to meet the state’s exacting standard.

“It’s a great approach, and potentially a game-changer,” said Elizabeth Wheeler of Clean Wisconsin, one of several conservation groups that have voiced support for the effort.

Some environmentalists remain wary because the phosphorus control measures aren’t guaranteed to be permanent. After a contract term of several years, farmers could decide to remove them if they are inconvenient or reduce income.

But Jeff Endres, a town of Springfield dairy farmer who has led a growing agricultural conservation movement in the Yahara River watershed, said he sees rising awareness of water quality issues.

Endres said he tells skeptics to consider that if voluntary measures don’t succeed, the federal government could force other solutions that cost more, as it has in areas that drain into the Chesapeake Bay on the East Coast. Fertilizer and manure runoff there have created a large “dead zone” in which aquatic life struggles to survive.

“I worry about that kind of thing damaging agriculture, dramatically affecting your yield,” Endres said. “It’s better having agriculture leading proactively instead of waiting and having things happen that can really have a negative impact.”

Nutrient pollution from Wisconsin contributes to two such dead zones, one in the Gulf of Mexico and the other in Green Bay, and hundreds of inland lakes and streams are classified as impaired because phosphorus has fueled unnatural algae and weed growth that limits swimming, boating and fishing.

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The “adaptive management” plan for the Yahara watershed was spearheaded by the Madison Metropolitan Sewerage District. It will reduce nutrient pollution more quickly and at lower cost to taxpayers than other available methods, said the district’s ecosystems service director Dave Taylor.

Instead of focusing on very expensive filtration systems to make limited reductions in waste water treatment plant discharges, the district will encourage and fund less costly efforts to reduce nutrient runoff from urban storm water and from farms, the source of most pollutants.

The result will be reduced pollution throughout the watershed, not just where the treatment plant discharges into Badfish Creek, Taylor said.

The program has a projected price tag of $104 million over its 20-year span. Taylor said taxpayers would pay about $270 million over the same time frame if the watershed’s three treatment plants and two dozen storm water systems took pollution-reducing steps that would be required if they were acting individually.

“The end result is expensive approaches that are unlikely to improve water quality throughout the entire watershed,” Taylor said of what might happen without the new program.

And as sources of pollution undertake costly or difficult phosphorus reduction efforts, they tend to blame their neighbors, suspecting that others aren’t doing their share, Taylor said.

“Our approach avoids finger-pointing and instead focuses on results,” Taylor said.

U.S. Environmental Protection Agency officials have said the Madison plan could become a national model if it succeeds. About 10 states permit similar programs but none with nearly as many municipalities and groups involved, the EPA said.

The EPA has urged states to create precise standards for how much phosphorus can be allowed in water. In 2010, Wisconsin was among the first in the nation to do so.

The state Department of Natural Resources phosphorus rule paved the way for the Yahara watershed project, which is one of just a handful that have emerged around the country to shift the fight against nutrient pollution from tightly-permitted sewers and industry to more loosely regulated farms.

With the passage of the federal Clean Water Act in 1972, industrial polluters and waste water plants were forced to sharply cut discharges through increasingly strict operating permits.

Now most phosphorus pollution comes from agricultural soil. But the law doesn’t require farms to have pollution discharge permits, in part because it may be more difficult to measure pollution coming from a field than from a pipe.

Under the adaptive management plan, the sewerage district’s operating permit will require phosphorus reductions not just from its discharge pipe, but across the watershed.

As with other runoff control grants, participation in the sewer district funding program will be optional for farmers, but will involving signing a contract.

The number of local organizations, environmental groups, farm organizations and others who have signed on to the Yahara watershed plan surprised the DNR, which developed the regulations that allow it.

“DNR never envisioned that adaptive management could be applied to a watershed this large or complex with so many diverse stakeholders,” said Kevin Kirsch, a water resources engineer for the agency. “This was no small feat and involved tremendous efforts on MMSD’s part.”

The Oconomowoc wastewater treatment plant has won approval for a smaller effort, and the Lodi sewage plant and the Dane-Iowa plant in Mazomanie are in planning stages, Kirsch said. The Madison adaptive management plan comes on the heels of a four-year pilot program that covered territory just northeast of Lake Mendota.

Denny Caneff, executive director of the River Alliance of Wisconsin, is a strong supporter of the plan, but he said he worries that results could suffer because runoff controls aren’t permanent. Some require that they be maintained for several years, but if corn prices rise and they want to plant more, farmers can plow the buffers under.

“Politically, (Wisconsinites) still have no appetite for regulating farmers, even the ones that violate pollution laws,” Caneff said.

A surer investment of tax dollars is the purchase of permanent conservation easements that prevent erosion of land around waterways permanently, Caneff said.

Taylor said he was optimistic that more and more farmers are seeing themselves as stewards both of the land and the water.

“One of the reasons that people are excited about the project is it’s a way to engage folks in a collaborative effort that’s never been done before,” Taylor said.

The DNR will issue a series of four five-year water pollution permits to the Madison sewer district with increasingly tighter limits on phosphorus for the watershed, Taylor said.

The last permit will require the concentration of phosphorus in water sampled from several locations to meet the state’s standard, Taylor said.

However, underwater sediment can be laced with high phosphorus concentrations that can be stirred up and released into the water.

If water samples don’t show standards are met, another option may be demonstrating through computer modeling that takes into account soil, water, weather and other conditions that the amount of new phosphorus entering the water each year had been decreased from the current 263,000 pounds to 157,000 pounds, the amount scientists say the water can absorb without problems.

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Steven Verburg is a reporter for the Wisconsin State Journal covering state politics with a focus on science and the environment as well as military and veterans issues.