In the world of Big Agriculture, Virgil Shockley is one of the little guys.

He and his wife own 84 acres in a rural hamlet in Maryland's Worcester County that is so small it doesn't even have a name. In a county synonymous with the bright lights of the Ocean City boardwalk, the road to Shockley's farm wends through forests and fields named for the families that have been working the land for generations.

Aside from a small Tyson logo affixed to the Boondock Farm sign along Shockley Road, there are no indications that a chicken house lies ahead. No telltale smells. No piles of manure outside. Just rows of neat gardens with wildflowers and melons and two long chicken houses, where the 45,000 birds who call this place home look clean, well-fed and even happy.

Two years ago, no one would have considered the Shockley farm a Concentrated Animal Feeding Operation, the government designation for a farm with so many animals that it is defined as a point source of pollution and regulated like one. But today, thanks to a set of 2008 regulations that redefined both pollution sources and animal operations, Shockley is among hundreds of Maryland farmers now regulated as CAFOs because they drain into state waterways.

The new definition affects many farms on the Eastern Shore that grow chickens, because the ditches that drain the farms lead into creeks and rivers.

In 2008, just 12 farms in the state were considered CAFOS. Now, the Maryland Department of the Environment estimates that 426 farms in the state will fall under the CAFO designation. The new rules, which changed in 2008, mean more paperwork, more stringent guidelines on manure storage and use, and probably more frequent visits by federal and state regulators.

Maryland is the first state in the watershed to have a federally approved CAFO program under the EPA's 2008 rules. But Pennsylvania and Virginia are working on tougher regulations. EPA inspectors recently made a visit to a watershed in Lancaster County and are focusing their efforts on a second one. Federal officials have also visited both Virginia's Eastern Shore and Shenandoah Valley.

EPA officials say the new regulations are needed to tackle one of the largest sources of pollution: manure coming from unregulated, smaller farms. Manure in the Chesapeake Bay is one of the largest sources of pollution, responsible for a fifth of the Bay's nitrogen and a quarter of its phosphorus. Classifying a farm a CAFO is one of the only ways that the EPA can extend its authority: Agriculture is exempt from regulation under the Clean Water Act unless the farms in question are CAFOs.

Jon Capacasa, director of water protection for the EPA's Region 3, which covers much of the Chesapeake Bay's watershed, said the goal is not to federalize all of the enforcement. But the EPA has made it clear it will exercise its authority. In particular, the EPA said it would include previously unregulated small farms that cumulatively can greatly affect local water quality.

"We know there are quite a few smaller operations that can have quite a big impact," Capacasa said. "We're not going to be successful without everyone in the (agriculture) sector doing their part."

Family farmers like Shockley bristle at the idea of being lumped in with industrial-size animal operations. They claim the added regulatory burden is only going to cost them time and money and will have no effect on pollution.

"What you have is a set of regulations whose purpose, and only purpose, is to control as many people as possible," Shockley said. "Don't let anyone tell you the result is about cleaning up the Bay. That's not the end result."

Some state regulators agree. Doug Goodlander, director of nutrient and odor management for the State Conservation Commission in Pennsylvania, said the commission is focused on smaller farms. But the problem is there are 63,000 of them, and only four state inspectors - if he can even maintain those jobs in the face of budget cuts.

What the EPA needs to do, Goodlander said, is stop generating new regulations and help the states enforce the ones already on the books. The agency can do that with more funds for inspectors and cost-share programs, and by working with state officials who understand the topography and hydrology of the landscape.

"It's unrealistic to think you can expand the permitting process when you don't have staff to do it, and you're not going to get any better water quality anyway," Goodlander said. "We're telling them, 'here's a better way to do it. You have to believe us.' But so far, they don't believe us."

That could change. The EPA is requiring states to submit plans this fall to show they have adequate staffing to administer their programs, or risk penalties.

But some Pennsylvania agriculture officials fear the new regulations will force farmers to consolidate under the weight of more paperwork, or go out of business altogether. Most of the farms in Pennsylvania are small dairies with about 60 milking cows, and they are struggling as it is with low milk prices.

But like them or not, Goodlander acknowledges, stricter federal regulations are probably coming. Indeed, they have been in the works for more than a decade.

The EPA had been discussing changes in its CAFO regulations for much of the 1990s. In 2003, the agency issued a new definition of a CAFO. If a farm raised more than 125,000 chickens, it was a CAFO. That applied to very few farms in the watershed. But the definition went a step further. It said medium-size farms - in the case of chickens, more than 37,000 birds - were also CAFOs if they discharged into waterways.

The 2003 regulations didn't change much right away. Farmers challenged it because they said it was too strong; environmentalists complained it wasn't strong enough; and state regulators didn't understand what the EPA meant by the word discharge.

The EPA spent the next several years attempting to clarify its position, according to David McGuigan, the agency's associate director of water protection. Meanwhile, Maryland decided to move forward on its own. In 2007, it created a MAFO designation - a Maryland Animal Feeding Operation. Working closely with the Delmarva Poultry Industry, a trade group, regulators decided that a farm had to have 75,000 chickens or more to be considered a MAFO.

All MAFOS would need nutrient management plans, but they could use the plans they already had; a CAFO designation would have required them to get new plans certified by a very small number of nutrient management plan specialists. MAFO rules also allow farmers to store manure outside for 90 days, whereas a CAFO allowed only 14 days.

The Waterkeeper Alliance, the New York-based environmental group that includes the riverkeepers who patrol the Chesapeake region, challenged the MAFO rules, just as they had challenged the EPA over the 2003 CAFO rules. In 2008, a court ruled that the MDE's definition could stand.

But the point was almost moot, because a 2005 federal court decision clarified the 2003 CAFO laws. With the legal challenges behind them, the EPA in 2008 put out a new set of regulations that federal officials say was more precise, but farmers and state regulators describe as far more restrictive.

In its 2008 regulations, the EPA said that Chesapeake Bay farmers had a duty to apply for federal CAFO permits if they discharged, regardless of whether they were large or medium size. If a farm with 37,000 or more chickens made any discharge into any conveyance (a ditch, swale or stormwater pond) that led to waters of the United States, they would be required to apply for a CAFO permit. Or if it didn't discharge now, but might in the future because of extreme weather events, it would require a permit as a CAFO.

Furthermore, if a farm raised fewer than 37,000 birds, but the EPA was concerned about its discharges, the agency could use its discretion to put that farm through a detailed analysis of its pollution and designate it as a CAFO at any time. As managers of CAFOs, farmers would now be required to make their nutrient management plans public. And the new CAFO rules also required nutrient management plans for applying manure, adding more regulatory burdens to the farmers.

"A lot of things that we were voluntarily creating this new program for, they became CAFOS. That, obviously, created a much broader universe," said MDE spokeswoman Dawn Stoltzfus, who counts 103 farms under the less-stringent MAFO designation. "Now, for the first time, we have over 500 farms being regulated, whereas before we had about a dozen. [The broadly inclusive regulation] levels the playing field for farmers who are doing the right thing, to make sure everyone is."

Unlike Maryland, Virginia had already been regulating most of its poultry operations since 2000. But the 2008 CAFO regulations required the state to make some changes. Every concentrated animal feeding operation that discharges or proposes to discharge now needs a federal permit, which includes a public application process. Virginia was able to get their state permit process approved under federal law, so Virginia farmers do not need to get new nutrient management plans, said Neil Zahradka, manager of the office of land application programs for the Virginia Department of Environmental Quality.

But the Virginia Pollution Abatement permit is a no-discharge permit, and that complicates matters, Zahradka said. Farmers can be covered under the state permit if they are not discharging at present, but if they discharge in the future they need the federal permit. A few feathers in a ditch is a discharge; so is a trench dug from a chicken house to a creek, or a stormwater pond that overflows in a freak rainstorm. The permit makes no distinction.

"One of the things we have struggled with is, it really doesn't matter how much. If any pollutants reach surface waters, that's a discharge," he said.

Pennsylvania is also questioning the EPA's new CAFO regulations. Under its Clean Streams Law, no one is allowed to discharge. So, state officials argue, they cannot issue a permit to a farm that proposes to discharge, because then that farm would be in violation of the Pennsylvania law. Of Pennsylvania's 64,000 farms, only about 1,000 are CAFOs. Those 1,000 farms are responsible for half the manure in the state, officials said. The rest of the farms need to have manure management plans if they use manure, but are not subject to stringent environmental regulations or inspections.

That changed in the spring, when the EPA unexpectedly inspected 25 dairy farms, most of them owned by Amish, in the Lancaster County area of Watson's Run. It found violations on 85 percent of them.

Pennsylvania officials said they have no plans to ramp up regulations on these farmers. Instead, the commonwealth wants to educate them on how, where and when to apply their manure, and what kind of paperwork to file.

"Those operations in Watson's Run that do not have a conservation plan or a manure management plan will get one. But they will get one under Pennsylvania regulations," said Don Fiesta, a hydrogeologist with the state's Department of Environmental Protection. "In other words, we are not going to go out and make them be CAFOs."

But the EPA's McGuigan said the violations at Watson's Run were more than just a lack of plans. Sixteen of the farms sampled had high levels of nitrates in their drinking water. One farmer told inspectors that he had installed a water treatment system because too many of his calves were born dead.

"We've had discussions with Pennsylvania on this," McGuigan said. "It's not realistic to say you will never discharge under any circumstance at any time, and therefore you don't need a permit, because we know that that is not true."

As he cradles one of his 3-week-old chicks, Shockley remembers the simpler times, when the respected county extension agent gathered farmers together at twice-annual chicken-and-dumpling dinners to impart the latest techniques for farming and raising animals. That was back in the days when raising chickens was a good stay-at-home job for his wife, Jeanne, who raised three children in between tending to the birds. Those were the days when the manure from the chickens was a resource he could spread on the field of his home farm as well as the 240 other acres he rents.

But in 2003, regulators were implementing a state law that required farmers to use both nitrogen and phosphorus-based nutrient management plans instead of plans based only on nitrogen. They measured his fields and found them too high in phosphorus. Shockley now has to spend about $24,000 a year on commercial fertilizer, while he sells the more phosphorus-laden manure for just $50 a load. To make ends meet, he has two other jobs: He drives a school bus and serves as a county commissioner.

He has put in conservation practices, such as buffers, but said that he doesn't take any government funds for them. He is building a second stormwater management pond, which will cost $5,000, even though he doesn't have to. He loves the land, which his family has owned for more than a century. And he loves the chickens. But every day, the 57-year-old asks himself how much longer he'll do it.

"You have a lot of people who have never been on a chicken farm making regulations for chicken farms, and that is the problem," Shockley said. "Quite frankly, the farmers are lost. They don't exactly know where to turn. They want to know, 'who has jurisdiction over what? How long can I leave manure in the field? Until I get arrested?' Is that the answer?"