The federal regulations also could require many to change their farming practices. The rules sharply restrict the amount of time they can stockpile manure in their fields before working it into the soil and require them to leave much larger swaths of land uncultivated along drainage ditches and waterways.
Anything the farmers report to the federal government is open to public inspection, which farmers have balked at in the past.
Scott Edwards, legal director of the Waterkeeper Alliance, welcomed the federal action. He said the rules should not be a great burden for farmers, and that the benefits for the bay are worth the costs of complying.
"To me, it's a no-brainer," he said. "You shouldn't be dumping your manure within a few feet of a ditch or gully that will carry it to a waterway. They can't do that - they should never have been able to do that."
State officials and farming representatives say the rush by Maryland farmers to get permits came after EPA officials reinterpreted a regulation, essentially declaring that if rainfall drains away from chicken houses into ditches and streams, it's likely carrying manure and needs to be controlled. Previously, almost all chicken farms had been considered exempt unless their animals were outdoors or the manure stored in lagoons.
"EPA's just really targeting poultry right now," complained Valerie Connelly, legislative director for the Maryland Farm Bureau.
But EPA officials counter that they are just clarifying a six-year-old regulation requiring pollution permits for many farms with large herds or flocks of animals, called "concentrated animal feeding operations," or CAFOs.
"CAFOs are a national priority for EPA, and they're also a regional priority due to the impacts on the bay," said David McGuigan, the agency's associate director of permits and enforcement for the Mid-Atlantic. "So we have to have a relatively aggressive compliance assurance program. Part of that is ... ensuring people obtain permits if they need them. A law that is not examined or enforced is a law that is not obeyed."
Shore farmers contend that the EPA is coming down harder on them than on chicken growers elsewhere. Rep. Frank M. Kratovil Jr., a Democrat who represents the Shore, said he has met with EPA officials to inquire if the policies are being applied evenly nationwide.
