Georgia farmers worried about the Environmental Protection Agency encroaching on their drainage ditches scored a partial victory in Congress’ $1 trillion spending package that was signed into law earlier this month.

But the EPA will move forward on a new regulation it says is crucial to limiting pollution in the nation’s waterways and will not overburden farmers, setting up a sure clash with the Republican majorities in the incoming Congress.

The dispute concerns a rule the EPA and the U.S. Army Corps of Engineers proposed in April to regulate tributaries to major waterways under the Clean Water Act — and a tributary does not necessarily have to flow year-round to qualify.

The farm lobby went on the attack against the “Waters of the USA” rule immediately, claiming that the EPA could take new jurisdiction over farmers’ property.

Jon Huffmaster, the legislative director for the Georgia Farm Bureau, said, for example, that the EPA could require a farmer to get a federal permit to drive a fertilizer spreader truck over a dry streambed that sometimes fills when it rains.

“It boils down to private property rights,” Huffmaster wrote in an email. “And our belief that this proposed rule infringes on those rights for no reason other than to make it easier for the federal agencies … to regulate us.”

The Georgia Farm Bureau's "Ditch the Rule" campaign funneled more than 15,000 comments to the EPA, part of a nationwide effort. The agency established its own pushback website called "Ditch the Myth."

The EPA says long-standing farming and ranching exemptions from Clean Water Act regulation will remain.

“The final rule will strengthen protection for the clean water that is essential to all Americans,” EPA deputy press secretary Monica Lee said in a prepared statement.

“Science clearly shows what kinds of streams and wetlands impact water downstream — the agencies are committed to protecting those waters. In fact, one in three Americans — that’s 117 million people – get drinking water from streams that are currently vulnerable and need clear protection.”

The spending law forced the EPA and the Army Corps of Engineers to withdraw an "interpretive rule" that the agencies intended to clarify the forthcoming water rule. The interpretive rule listed 56 farming practices that would not be affected by the rule.

But farmers objected because the 56 practices were exempt only if they met conservation standards from the U.S. Department of Agriculture’s Natural Resources Conservation Service, which they said would bring a new layer of clean water regulation.

“It totally changes the purpose of NRCS,” Huffmaster said.

Jennette Gayer, the director of Environment Georgia, called yanking the interpretive rule the “first volley” of the coming fight over the water rule in Congress.

“We’re glad the clean water rule is still out there, and we think we can get the protections that we need,” Gayer said, “but certainly this was a not a good thing.”

The spending bill was one of the final acts of the split Congress. When Republicans take over the Senate next year, the balance of power will shift more firmly against the EPA.

Even with Democrats still clinging to the Senate this month, the compromise spending bill had several elements targeting the EPA, including a $60 million budget cut that is expected to bring the agency’s staff to its lowest level since 1989.

Many Republicans were dissatisfied with parts of the bill, but the EPA attacks were a tasty carrot to vote for it. In its work, including water and air pollution regulations — the agency's plans to limit carbon emissions angered utilities — the agency has been more aggressive in Obama's second term, with Republicans eager to fight back.

“We’ve got a lot of good stuff in the bill — policy riders and things that we’ve been fighting for for years,” said Republican U.S. Rep. Doug Collins of Gainesville, who voted for the spending bill. “When you go back at the EPA being (staffed at 1989) levels, these things are a success for us.”

Republican U.S. Sen. Johnny Isakson of Georgia supported the bill in the Senate, in part because of the Waters of the USA language, which he said is “huge for Georgia.”

“It’s the No. 1 issue of agriculture, and, quite frankly, in road construction and development in Atlanta it’s the No. 1 issue,” Isakson said.

“Because if we didn’t get Waters of the USA fixed in terms of what the EPA wanted to do, EPA would be able to shut down every farm and every construction project in the state of Georgia and you just don’t want that to happen.”

The EPA contends that its foes are being hyperbolic, and it’s not backing away from its plans to finalize the water rule in the first half of 2015.

The interpretive rule “was intended to encourage conservation and provide farmers with a simpler way to take advantage of existing exemptions from Clean Water Act dredge and fill permits,” said Lee, the agency’s deputy press secretary.

“Normal farming and ranching — including planting, harvesting and moving livestock — have long-standing exemptions from Clean Water Act regulation, and withdrawal of the interpretive rule will not change those historic exemptions or the agencies’ work to finalize the Clean Water Rule.”