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TOWN OF LINCOLN - Lee Kinnard’s new barn stretches the length of six football fields. It’s so big he once flew a drone inside to get a bird’s eye view of all the cows.

The family farm milks 6,500 cows in Kewaunee County, where the cattle population has grown faster than anywhere in the state.

Since 1983, cattle numbers in the county have jumped by 62% to 97,000 at a time when the statewide cattle population has tumbled by 20%, according to the state agriculture department.

Dairying here is thriving. But the size of dairy herds and managing cattle waste have become increasingly contentious in northeastern Wisconsin and figure prominently in a larger debate over how best to address water problems tied to farming.

Tucked beneath Door County, Kewaunee County has emerged as the flash point in these tensions. At the heart of the debate: Can manure from so many cattle be safely spread on the land?

“Absolutely, I think that agriculture and the environment can go hand-in-hand,” Kinnard said.

Kinnard, 48, speaks with a preacher’s reverence for farming and believes technology and good management can keep problems at bay.

He describes manure as “organic material, the lifeblood of soil.” Despite all the waste his cows produce, the manure he spreads supplies only half of the fertilizer for 13,000 acres.

The farm — owned by Lee, his brother, Rod, and Rod’s wife, Maureen — has grown dramatically since 2000 when there were 350 milking cows.

But becoming one of the state’s largest dairy farms has wounded relations with some neighbors and spurred a protracted court fight. Also, by virtue of its size and the attention it receives, Kinnard Farms has helped fuel controversy over truck traffic, odors and pollution from farming when it is done on a grand scale.

“For people living on these roads their whole lives, it isn’t what they are used to,” said Nick Cochart, a neighbor of Kinnard’s and superintendent of Algoma’s public schools. Speeding trucks and farms that seem more like industrial sites have upended rural life, he said. “To be honest, it’s beyond frustrating,” he said.

Lee Luft, a retired executive and a member of the Kewaunee County Board, said farming and water pollution have become inextricably tied in local politics.

“There’s simply too many cows,” he said.

Kewaunee County ranks third with 16 mega-sized dairy farms. Neighboring Brown leads the state with 20 and Manitowoc follows with 18, according to Department of Natural Resources figures.

In Wisconsin, the number of concentrated animal feeding operations, or CAFOs, has grown by 400% from 50 in 2000 to 252 in 2016, agency figures show, and has played a key role in growing milk production as farm numbers are falling.

In a report, University of Wisconsin-Madison economists estimated that farms of 500 or more cows accounted for 40% of state milk production in 2013 compared to 22% in 2007.

Big farms’ share of the milk supply has grown since then and the trend is expected to continue because of the advantage of scale in producing a basic commodity, said Mark Stephenson, director of dairy policy analysis at UW-Madison.

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The Kinnard dairy farm in Kewaukee County milks 6,500 dairy cattle through a CAFO (concentrated animal feeding operations). The county has a problem with contaminated wells but the Kinnards say their precise manure measurement prevents run-off. Rick Wood/Milwaukee Journal Sentinel

The challenge in Kewaunee County is the region's fractured bedrock can allow water and manure to seep into groundwater if there are no safeguards.

The county’s three major rivers — the  Ahnapee, East Twin and Kewaunee — all violate state standards for phosphorus pollution. Manure is a source of phosphorus. In excess, it promotes algae blooms. The rivers were placed on a state list of impaired waters in either 2014 or 2016.

Alarmed by reports of polluted wells, Kewaunee County residents in 2015 voted overwhelming to support an ordinance restricting manure spreading in winter and early spring on fields with 20 feet or less of soil.

It was the first time a Wisconsin county took such action.

The DNR's wastewater program, which includes CAFOs, came under fire by the independent Legislative Audit Bureau last year because of backlogs, staff turnover and other problems. Auditors noted CAFOs pay a single annual fee of $345 — the DNR receives $95 from it —  while wastewater utilities pay thousands of dollars. The City of Waukesha, for example, paid about $12,000 last year.

When the Natural Resources Board grilled DNR Secretary Cathy Stepp last June over the audit, board member Frederick Prehn of Wausau said the fee structure was out of whack. "That in all basis is not fair," he said. "It doesn’t make any logical sense to the taxpayer."

CAFO critics wanted higher fees for big farms. But Republican Gov. Scott Walker did not boost the fees in his budget, which is now before lawmakers. Walker did propose a study that could turn over regulation of CAFOs to the state agriculture department — a measure pushed by a farm group, the Wisconsin Dairy Business Association, and opposed by environmental groups.

In November, Walker traveled here and announced plans for private-sector initiatives to biologically treat animal waste and capture the methane to produce energy. The administration is earmarking $20 million in subsidies to rid pollutants from manure. Kewaunee County is expected to be a leading candidate for such a project.

It’s a high-profile initiative for Walker at a time when those who want limits on spreading are criticizing his administration for inaction.

In 2014, six environmental groups petitioned the U.S. Environmental Protection Agency to investigate groundwater contamination in Kewaunee County, arguing the DNR had been slow to respond.

As a response, the DNR organized a task force on groundwater issues that met for a year and led to a series of recommendations including stricter controls on manure spreading.

But clean-water advocates had expected more.

By the time the Natural Resources Board had approved plans in August for new rules on manure spreading, tougher measures and specific requirements on CAFOs had been removed after farm groups appealed to Walker and the DNR.

“We’re not looking at the full package of rules the department put together,” griped Jennifer Giegerich, legislative director for the Wisconsin League of Conservation Voters, at a packed meeting in Ashland.

It might not be what environmentalists wanted. But lobbyist John Holevoet said the DNR will still target pollution-prone areas.

“We are hoping we get this done in a more efficient and less acrimonious way,” said Holevoet, director of government relations for the Wisconsin Dairy Business Association.

With Kewaunee County's nearly 100,000 cows, residents have been plagued by polluted wells. Blame has long been directed at farmers — but not always justified.

In February, in the most rigorous study to date, manure and human waste were found to both be sources of groundwater pollution.

Microbiologist Mark Borchardt of the U.S. Department of Agriculture used DNA sequencing to tease out bacteria and viruses in tap water from 82 wells. He found farms and malfunctioning septic systems both are culprits.

In one case, results showed it was manure polluting Erika and Rob Balza’s well near Luxemburg.

A farmer had been spreading manure next door. Then it began to rain.

On the evening of Oct. 26, 2016, “I turned on the sink faucet to brush my teeth — it came out brown,” Erika Balza said. “Rob turned on the water in the shower to get it heated up. The water was a brownish black color and immediately smelled of manure.”

The farmer was cited for illegally spreading manure and prohibited from spreading on the field again, according to DNR records.

His small farm is a far cry from Kinnard's sprawling operation.

“There is a broad painting of the brush that big is bad,” Kinnard said. “I don’t think that we are very good at communicating our story.”

From Kinnard’s conference room, visitors can watch cows being milked in an automated milking parlor that processes 650 cows an hour and operates virtually around the clock.

About a quarter of his 82 full-time employees has post-secondary education in agronomy, animal science or related fields. The CAFO allows him to invest in technologies that lighten the farm's impact, he said.

To ensure manure is applied optimally, Kinnard has mapped fields with sonar-like equipment that measures soil depth over bedrock. Any field with less than 3 feet of soil is avoided, he said.

But problems do occur.

DNR records show at least four infractions since 2010 after workers spread manure improperly — once near a stream and another time on land with sinkholes, which can have direct contact with groundwater. Kinnard acknowledged the mistakes.

“It shows you the system works,” he said. “If something goes wrong, you make it right.”

Kinnard and his farm drew statewide attention in 2014 when a state administrative law judge, in a case with many twists and turns, approved his plans to increase by 2,000 cows to 6,500 cows.

But in doing so, Judge Jeffrey Boldt said polluted wells in the region were well-documented and that "more likely than not that some portion of this contamination is from CAFO land-spreading."

“The proliferation of contaminated wells represents a massive regulatory failure to protect groundwater in the Town of Lincoln,” he wrote.

Kinnard’s approval included conditions that set a limit on the number of cows and required groundwater monitoring to identify elevated levels of bacteria.

“That was a big win for the people of Kewaunee County,” said Sarah Geers, an attorney for Midwest Environmental Advocates.

Kinnard appealed, which was denied by the DNR.

But eight months later, Stepp, a Walker appointee, sent a letter to the Department of Justice and asked whether the DNR had the authority to impose the conditions.

A day later, Republican Attorney General Brad Schimel’s office said the DNR did not.

Environmentalists appealed the case, and won, and the case is now before the state court of appeals.

The expansion went ahead.

“The process has been very frustrating,” Kinnard said. “It basically puts a family business into a position that they are guilty until proven innocent.”

But Geers sees it differently.

“Once a farm like Kinnard becomes a large industrial facility with hazardous waste, we need to hold them accountable,” she said.

Kevin Crowe of the Journal Sentinel contributed to this story.

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