The pollutant most regulators focus on is nitrate. At high levels in drinking water, nitrate can cause methemoglobinemia, or blue baby syndrome, where nitrogen compounds interfere with the blood's ability to carry oxygen. Formula-fed infants are particularly susceptible. Possible effects of chronic high nitrate exposure on adults include cancer, reproductive problems and diabetes, although researchers say more study is needed.

Nitrate is not necessarily the most dangerous substance given off by Concentrated Animal Feeding Operations, or CAFOs. But it is one of the few manure pollutants the government has the authority to regulate. The federal Safe Drinking Water Act limits nitrate concentration to 10 parts per million. That law, which applies to all drinking water systems serving more than 25 people, and the Clean Water Act, which regulates water quality for pollutants like phosphorous, nitrates and E. coli in surface water, are the main tools regulators can use to curb pollution from factory farms; the majority of air and water contaminants produced by CAFOs are not federally limited.

States can go beyond federal law to curb CAFO pollution, however. New Mexico, for example, has a water-quality act that protects groundwater and stipulates that all facilities whose waste may end up in groundwater -- including dairies -- must get discharge permits.

Kathy Martin, an engineer from Oklahoma, has consulted for over 15 years on technical aspects of rulemaking in 20 states, including Kansas, Colorado, Nebraska and New Mexico. She's watched residents protest against odor and flies; worry about CAFO-caused air pollution, a major health problem that is virtually unregulated; and fight to protect their drinking water. In her opinion, none of the states where she has worked has adequate rules to protect the health of dairy neighbors and the environment. "Industry almost invariably gets their way," she says. "Very rarely do the citizens get their way even on one or two points. We're just there to keep the dam from completely falling apart."

Because of New Mexico's water-quality act, the state has been monitoring pollution from dairies since about 1980, shortly after the first of several California dairies moved to a depopulated stretch of U.S. Route 80, now Interstate 10, between Las Cruces and the Texas border. Today, over a dozen dairies and tens of thousands of cows crush together along a 10-mile stretch of highway here that locals call Dairy Row.

In areas around Dairy Row, nitrate levels in drinking water exceed safety standards, and many people purchase bottled water. In 2007, the federal Environmental Protection Agency accused 11 local dairies of violating the Clean Water Act by not keeping proper records on waste management and disposal, and ordered them to comply immediately.

Martin sees better regulations as an issue of fairness, particularly for the rural and low-income areas where such facilities tend to locate. "If I find out that the mozzarella cheese in my pizza comes from a facility that has destroyed the groundwater for fifth- and sixth-generation Hispanics in New Mexico, it makes me sick to my stomach. ... I thinkat the end of the day, everyone would like to go to bed knowing that there isn't one person suffering, or child ill, because I had a Big Mac today."

Jerry Nivens already knew what keeping so many animals in one place could do. Years ago in Texas, he'd lived near giant beef feedlots in the Panhandle and around dairies near Waco, where he'd seen rivers polluted and towns filled with the stench of untreated manure. (In 2004, Waco sued 14 dairies for polluting the town's drinking water.) Thinking about ParaSol, he says, "I couldn't hardly sleep at night. Things like this are such a destruction to the surrounding area and the environment, you know, they create a sacrifice zone."

He called the state's Environment Department and learned that officials, who had never denied a permit before, did not plan to do so with ParaSol. In New Mexico, however, the environment secretary must sign off on all such permits. This gave Nivens, who had organized a group called Caballo Concerned Citizens and allied with the Rio Grande chapter of the Sierra Club, a wedge. Members sent more than 400 letters to the agency and visited New Mexico Environment Secretary Ron Curry, a Bill Richardson appointee, in person, asking him to say no to ParaSol.
And in February 2008, Curry did.

Nivens was ecstatic. He had no way of knowing this was just the beginning of a nearly four-year fight.

ParaSol immediately hired Pete Domenici Jr., a powerful lawyer and son of a former U.S. senator from New Mexico, and appealed the decision. Dairy owners formed a lobbying organization called Dairy Industry Group for a Clean Environment, backed by the national Dairy Farmers of America. By early 2009, the group, whose lobbyists included former Lt. Gov. Walter Bradley, had pushed the Legislature to amend the state's water-quality act to require the Environment Department to create a new, standardized permit process. The dairy owners were betting it would work in their favor.

"The environment at that time was one of constant change (for dairy permits)," says New Mexico state Sen. Clinton Harden, R, who sponsored the legislation amending the act. That uncertainty made it hard for new dairies to start up and existing ones to expand, he says. During that time, at least three dairies -- important employers and economic engines in his eastern district -- had moved to Texas, which had "a known permit process."

But the dairymen hadn't counted on Bill Olson. Olson, a hydrologist and 25-year veteran of the Environment Department, was the chief of New Mexico's groundwater division. He exudes the patience and practicality of your ninth-grade chemistry teacher, but with a Western flair: The day I met him at a Santa Fe bakery, he was wearing cowboy boots, jeans, a pearl-button shirt and a bolo tie.

"Ninety percent of all our drinking water in the state comes from groundwater," he explained. Though he would retire almost as soon as the process was over, he viewed the rulemaking as a chance to "prevent pollution and protect the resource."

Olson's department drafted a preliminary rule with two key requirements. To get a permit, dairies would have to install monitoring wells upstream and downstream of their manure lagoons. They'd also have to install high-density polyethylene synthetic liners.

The latter are much more effective at containing pollutants than traditional clay liners. And the wells would let the Environment Department know if groundwater was becoming contaminated. Because wells would be located both above and below lagoons, they'd help regulators triangulate on the source of any contamination. Most states don't directly track dairy waste this way. Regulators may believe a dairy has contaminated groundwater, but without a way to pinpoint the source, blame -- and responsibility for cleanup -- often gets passed around.

Starting in May 2009, the New Mexico Environment Department held meetings to get public comment on the draft rule. Angry dairy owners boycotted. But Jerry Nivens had spent months creating an activist network, meeting with grandmothers from Dairy Row whose children couldn't play outdoors because of flies, and a mom from the faraway town of Hobbs who blamed her kids' illnesses on high levels of nitrates in her drinking water. Nivens organized these people and allies from his earlier efforts under the name New Mexicans for Dairy Reform and formed alliances with a local water protection nonprofit called Amigos Bravos, as well as the national consumer advocacy group Food and Water Watch. The New Mexico Environmental Law Center, a nonprofit law firm specializing in environmental justice issues, represented the group during the rulemaking.