Over its long history, the American Farm Bureau Federation, a powerful national lobby, has paid little attention to the Chesapeake Bay region, which includes the District, Virginia and Maryland.

But at its annual conference in Atlanta last month, the group issued a call to arms against the Environmental Protection Agency’s plan to limit the amount of toxic pollutants that flow into the bay from cities and farms and suffocate marine life.

The Farm Bureau recently filed a lawsuit in federal court in Harrisburg, Pa., to stop the EPA. It argued that the bay’s cleanup is the responsibility of the six states in the region and that the EPA does not have the authority to establish a “pollution diet” that will cost taxpayers and farmers billions of dollars by the time it is fully implemented in 2025.

The lawsuit also says that the EPA’s science in determining the level of the bay’s pollutants is flawed and that the agency did not allow sufficient public comment in the run-up to the plan’s implementation in December. The Pennsylvania Farm Bureau is a co-plaintiff in the lawsuit, and local governments in the Hampton Roads area of southern Virginia are contemplating their own suits, according to reports.

Why is the American Farm Bureau so concerned about the Chesapeake Bay? And why now?

The farm lobby has made it clear it sees the cleanup effort as a harbinger of more far-reaching EPA requirements across the country, including in the Mississippi River basin, where chemical runoff from industrial farms is swept to the Gulf of Mexico. This pollution creates large swaths of low-oxygen areas known as dead zones, killing marine life.

“This new EPA approach will not end with the Chesapeake Bay,” Bob Stallman, the Farm Bureau’s president, said in an address early this month. “EPA has already revealed its plan to follow suit in other watersheds across the nation, including the Mississippi watershed. That is why our legal effort is essential to preserving the power of the states — not EPA — to decide whether and how to regulate farming practices in America’s watersheds.”

An EPA spokesman declined to comment on the litigation but said restoring the bay to health will help local economies and encourage recreational activities.

Environmentalists are concerned that the Farm Bureau is focusing on the cleanup of the Chesapeake Bay watershed because of its broader interests in the Midwest. Don Carr, a spokesman for the Environmental Working Group, which monitors the Farm Bureau, said the lawsuit is a warning to stay away from the Mississippi River basin and the giant farms around it.

The EPA put its latest pollution diet in place in December, calling it the largest water pollution strategy in the nation.

“I agree that this is motivated by the national Farm Bureau’s issues elsewhere. The Chesapeake Bay just happens to be the place where [regulations] are being implemented now,” said Sen. Benjamin L. Cardin (D-Md.), noting that bay enforcement efforts have been around for 10 years.

Cardin said the lawsuit lacks merit because each state, not the EPA, designs its own cleanup plan.

The Chesapeake Bay is the nation’s largest estuary. A 2003 report by the Chesapeake Bay Watershed Blue Ribbon Finance Panel chronicled its decline from overfishing and pollution and pointed to the drop in oyster harvests in Virginia. In 1984, watermen captured 4 million pounds of the crustacean. In 2003, they harvested only 77,000. There were 200 shucking houses in the mid-1980s. In 2003 there were 20.

Taxpayers and businesses in Virginia and Maryland will pay up to $20 billion over the next 15 years to implement the EPA’s pollution diet, formally known as the Total Maximum Daily Load of sediment, nitrogen and phosphorous being washed into the bay.

Rep. Bob Goodlatte (R-Va.) said he supports the Farm Bureau’s effort to halt the EPA limits partly because of the cost. Goodlatte, who drafted House legislation to strip the effort of funds, called the EPA’s actions “overzealous” and said they were taken “without a cost-benefit analysis to determine the overall cost of these mandates or even whether or not they will benefit the bay.” Goodlatte said the states in the Chesapeake Bay region “know better how to manage a state’s water quality goals than the bureaucrats at the EPA.”

But W. Tayloe Murphy Jr., a former member of the Virginia House of Delegates and a former state secretary of natural resources, said the need for EPA action was clear decades ago.

“I’ve lived in the bay region for 78 years, and I have watched a thriving industry for fish and crabs die because of our failure to keep the habitat clean,” Murphy said. “We’ve ignored the problem for 30 years, and now we’re paying the price. If you don’t have some type of leadership of the [cleanup] program, things just don’t get done.”

In a statement, Virginia’s current natural resources secretary, Doug Domenech, declined to comment on the lawsuit, saying he has not read it. But his frustrations with the EPA’s pollution diet, as well as Republican Gov. Robert F. McDonnell’s, align with the Farm Bureau’s arguments.

“We understand the frustration of the states working with EPA on this,” Domenech said. “Governor McDonnell has expressed concerns with the timing, legality, costs, and questionable science associated with EPA’s implementation” of the bay cleanup plan.

Bob Summers, acting secretary of the Maryland Department of the Environment, said the state set its own clean-water standard.

“Maryland is implementing its own plan, as are other states,” Summers said. “I think, clearly, EPA has given us our assignment, and they have said we can achieve that goal by any combination of things that we want. We just have to achieve the goal.”

Without the EPA, the cleanup of the bay’s waters would lack cohesiveness, Summers said.

“Maryland cannot restore the bay on its own,” he said. “It only controls a small part of the watershed. We need other states to do their jobs as well.”