After Hurricane Matthew churned across North Carolina earlier this month, swollen rivers deluged poultry and swine farms, killing millions of chickens and thousands of hogs and sending potentially toxic animal waste coursing into waterways.

It could take weeks or months for North Carolinians to learn the scope of the pollution or where it came from—if they ever do.

"We may never know how bad this was or the extent of the damage," said Travis Graves, a North Carolina-based member of the Waterkeepers Alliance, who has been surveying the scene from the air. "The state doesn't even know how big the poultry industry is here."

Thousands of industrial farms across the country release contaminants into the nation's water and airways, but in many states like North Carolina, the public has limited access to information about them. Federal authorities can't gauge the scope of the pollution, either, because in some states they have very little idea of the number and location of farms. This makes regulatory oversight weak and in some cases, nonexistent.

"You can get this information on coal plants or any other polluter," said Tarah Heinzen, an attorney with Food & Water Watch, an environmental advocacy group that has called for the agency to submit information about CAFOs to the public. "But you can't for this industry."

These massive farms, or CAFOs—Concentrated Animal Feeding Operations—can house hundreds of thousands of animals in confined spaces, creating potent volumes of nutrient pollution that have fouled rivers, lakes and oceans. Decomposing manure releases toxic chemicals, mostly ammonia and hydrogen sulfide, into the air. Manure stored in lagoons releases methane and nitrous oxide, global warming gases more powerful than carbon dioxide.

The Environmental Protection Agency has estimated that about 11 percent of the greenhouse gas emissions in the U.S. come from agriculture, and about 12 percent of total methane emissions comes from manure management, a rise of about 65 percent since 1990.

In a Regulatory Vacuum

The EPA, which regulates CAFOs under the Clean Water Act, puts the number of CAFOs at about 19,200, up from about 3,600 three decades ago. But environmental groups say that number is probably higher, largely because the agency has been unable to get reliable and comprehensive information, thanks to patchy state regulation and years of legal pushback from the livestock industry to keep the information from the public.

"The EPA doesn't really know where the CAFOs are," Heinzen said. "That's a huge problem. And this is 40 years after the Clean Water Act, and this industry has exploded."

The latest decision in a long-running legal war over CAFO information disclosure came last month when a federal appeals court ruled that the EPA violated the privacy of CAFO operators by releasing information about their farms, which had been requested by three environmental groups through the Freedom of Information Act in 2013. The ruling was a victory for the $186 billion meat-and-poultry industry, but environmental groups say it prevents the agency from better regulating CAFOs, at a time when a boom in construction may be on the way.

In North Carolina, state regulators exempt poultry CAFOs from public records disclosure, but earlier this year, environmental groups revealed there are about 3,900. They mapped them out for the public to see for the first time. (The state does disclose locations of cattle and swine CAFOs.)

"There's a lot of piecemeal information out there and the whole system is set up for these facilities to operate without any hindrance," said Christian Breen, a field specialist with the Waterkeeper Alliance's North Carolina office. "We just want the information to get to the public."

The EPA referred questions about CAFO regulation to the Department of Justice, which did not return requests for information. The American Farm Bureau Federation, the nation's largest farming organization, meanwhile, says it does not oppose giving information to the states and to the EPA.

"Each state is unique, but states generally do have the locations of CAFOs within their borders, and many have robust state programs that govern those farms," said Ellen Steen, an attorney with the Farm Bureau. "AFBF does not oppose state or EPA collection of information associated with CAFOs to aid in their implementation of their programs, but once gathered, that information should be treated with care to protect the privacy of individuals and to protect the food supply."

Bigger Farms, and Problems, Ahead

As demand for protein climbs, particularly in developing countries, and U.S. meat exports rise, the number and size of CAFOs will likely rise, too. That could have major consequences, from rising methane emissions from manure lagoons to increased releases of nitrous oxide from fertilizer used to grow feed. Environmental groups, already alarmed about what they see as a lack of pollution regulation in agriculture, say this expansion makes government oversight and public disclosure all the more critical.

"If you look at the trajectory over the last 20 years, it's going in one direction and it's going there fast. It's terrifying to watch," said Abel Russ, an attorney with the Environmental Integrity Project, which has sued the EPA for CAFO information. "They just keep getting bigger and more concentrated. There's no limiting factor."

Iowa, the state with the most CAFOs in the country, has a "work plan" with the EPA to improve improve regulations, but in its latest annual report, the state's Department of Natural Resources said it had identified more than 5,000 feeding operations "that need further investigation to determine their regulatory status." Of those 5,000, the department estimated as many as 1,266 could be big enough to classify as CAFOs, but none are in the EPA's tally.

"That underscores just how spotty the data on the industry are," Heinzen said, "and EPA is relying on states to cobble together its own national database."

Starting in the 1950s, more livestock producers brought their animals indoors, into large, more efficient barns. These intensive confinement operations made it easier to care for animals, get them to market weight and satisfy demand for protein, but they also presented a big challenge in disposing of massive amounts of manure.

Most CAFOs, about 90 percent according to the EPA, hold manure in lagoons, before applying it onto fields. When that application is done properly, the manure acts as a fertilizer, regenerating the soil. But when it's done improperly, the runoff — specifically the phosphorus and nitrogen in it — can pollute waterways and leach into groundwater.

Spills Prompt First Attempts to Regulate

In the 1990s, a series of nightmarish incidents occurred at CAFOs around the country, including in North Carolina, where millions of gallons of liquid hog waste spilled into rivers, tributaries, swamps and wetlands, causing drinking water contamination and fish kills. Several environmental groups filed lawsuits, ultimately pushing the EPA to tighten regulations.

The EPA agreed to set new effluent limitations, and in 2003 issued a rule that required, for the first time, that all CAFOs apply for discharge permits unless they could prove they didn't have the potential to pollute.

The livestock industry, led by the American Farm Bureau, the National Pork Producers Association and the National Chicken Council, argued that the Clean Water Act authorized the agency to require a discharge permit only if there was actual discharge, not potential discharge, as the EPA rule stated. A federal appeals court ultimately agreed.

The EPA tried again in 2008, issuing another rule requiring CAFOs to obtain permits if they "discharge or propose to discharge" pollutants.

Both the livestock industry and environmental groups immediately responded with legal challenges.The environmental groups argued that the rule allowed CAFO operators to determine whether they "discharge or propose to discharge," and also failed to provide oversight of those assertions. The livestock industry, once again, argued that the EPA only has authority to regulate actual discharges, not proposed or potential ones. A federal appeals court again agreed with the industry, saying the agency had overstepped its authority.

The environmental groups agreed to a settlement that ultimately required the EPA to issue yet another rule—this one, a "reporting rule" requiring CAFOs to submit certain basic information to the agency to obtain discharge permits under the Clean Water Act.

In 2011, the EPA proposed that rule, but after getting strong blowback from the industry citing privacy violations, the Obama administration scrapped it.

"We don't want them to have a big database of where all these farms are," said Michael Formica, an attorney for the National Pork Producers Association. "There's on-farm security, national security, implications. So we stopped the rule. The USDA, the FBI were behind us. They said: You can't do this rule. You can't create this database, because you're going to give a roadmap to terrorists, to animal activists."

Instead, EPA made an arrangement with states to collect the information, because those details—like location and number of animals—are needed to determine which operators need permits and which CAFOs were violating the law. The agency has estimated that as many as 75 percent of CAFOs needed permits because they discharge as a result of their standard operational profile, but that only 40 percent actually have them.

Environmental groups, skeptical that the EPA was collecting information from the states, filed a request under the Freedom of Information Act to see if the EPA was holding up its end of the agreement.

"They wanted to see how that process was going," Heinzen said. "They filed for the CAFO information that EPA got through this process to see if the process was working."

The agency released the information in response to the request, which included home addresses, GPS coordinates, private phone numbers and email addresses. But the industry challenged it and an appeals court ruled last month that the EPA abused its discretion and private information should have been exempt from the Freedom of Information Act.

"This is not a CAFO issue," said Danielle Hallcom Quist, a senior attorney with the American Farm Bureau Federation, a plaintiff in the case. "This lawsuit is about whether the federal government, not just EPA...can use its information-collection authorities, which the government has a lot of, to collect personal information from state regulators, compile that information and then hand it off."

Pollution vs. Privacy

The environmental community now finds itself in a familiar position.

"The court found there was a privacy interest. What about the public interest?" Heinzen said. "The public interest is that this information sheds light on the agency. We need to know what it's doing. We need to watchdog EPA's efforts, and the court didn't buy that."

The livestock groups say they'll continue to press for privacy.

"I don't know about the coal or gas industry, but the difference here is that farmers live on these farms," Hallcom Quist said. "These are family farmers. There are multiple generations living on these farms. The family house is a stone's throw from the barn. Should the public have a blueprint on how to call individual farmers in their kitchens?"

Environmental groups say the answer is yes, because CAFOs carry too many health and environmental risks for them to operate in the regulatory dark.

"If someone wants to run a daycare out of their home, you don't allow them to keep information about children from the public," Heinzen said. "If you chose to live at your business, that shouldn't prevent the public from getting information about water, air, or their quality of life."