Nearly 40 years after the first Earth Day, this is irony: The United States has reduced the manmade pollutants that left its waterways dead, discolored and occasionally flammable.

But now, it has managed to smother the same waters with the most natural stuff in the world.

Animal manure, a byproduct as old as agriculture, has become an unlikely modern pollution problem, scientists and environmentalists say. The country simply has more dung than it can handle: Crowded together at a new breed of megafarms, livestock produce three times as much waste as people, more than can be recycled as fertilizer for nearby fields.

That excess manure gives off air pollutants, and it is the country’s fastest-growing large source of methane, a greenhouse gas.

And it washes down with the rain, helping to cause the 230 oxygen-deprived “dead zones” that have proliferated along the U.S. coast. In the Chesapeake Bay, about one-fourth of the pollution that leads to dead zones can be traced to the back ends of cows, pigs, chickens and turkeys.

Despite its impact, manure has not been as strictly regulated as more familiar pollution problems, like human sewage, acid rain or industrial waste. The Obama administration has made moves to change that but already has found itself facing off with farm interests, entangled in the contentious politics of poop.

In recent months, Oklahoma has battled poultry companies from Arkansas in court, blaming their birds’ waste for slimy and deadened rivers downstream. In Florida, the U.S. Environmental Protection Agency proposed first-of-their-kind limits on pollutants found in manure.

In the Senate, Benjamin L. Cardin (D-Md.) has proposed a bill that would allow farmers in the Chesapeake watershed to cut pollution more than required and sell the extra “credits” to other polluters. The EPA, in the middle of an overhaul for the failed Chesapeake cleanup, also has threatened to tighten rules on large farms.

“We now know that we have more nutrient pollution from animals in the Chesapeake Bay watershed” than from human sewage, said J. Charles Fox, the EPA’s new Chesapeake czar. “Nutrients” is the scientific word for the main pollutants found in manure, treated sewage, and runoff from fertilized lawns. They are the bay’s chief evil, feeding unnatural algae blooms that cause dead zones.

Around the country, agricultural interests have fought back against moves like these, saying that new rules on manure could mean crushing new costs for farmers.

“It’s clearly going to put a squeeze on people that they’ve always said they didn’t want to squeeze,” including family-run farms, said Don Parrish of the American Farm Bureau Federation.

The story of manure is already a gloomy counterpoint to the triumphs in fighting pollution since the first Earth Day in 1970. An air pollutant that causes acid rain has been cut by 56 percent. By one measure, the output from sewage plants got 45 percent cleaner.