Organizations representing American farmers slammed a recent Biden administration regulation repeals a Trump-era action regarding how natural water sources in the U.S. are protected.

The groups argued that the rule would increase uncertainty and pose regulatory roadblocks for farmers. On Friday, the Environmental Protection Agency (EPA) finalized the rule change, redefining which "waters of the United States" are federally protected under the Clean Water Act. 

EPA Administrator Michael Regan said the regulation change "safeguards our nation’s waters, strengthens economic opportunity, and protects people’s health." But critics of the move said it would lead to increased federal scrutiny of how farmers and other landowners treat water sources on their property such as ravines and creeks, creating additional costs.

"AFBF is extremely disappointed in the EPA and Army Corps of Engineers’ new Waters of the United States Rule," said Zippy Duvall, the president of the American Farm Bureau Federation. "Farmers and ranchers share the goal of protecting the nation’s waterways, but they deserve rules that don’t require a team of attorneys and consultants to identify ‘navigable waters’ on their land." 

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"EPA has doubled down on the old significant nexus test, creating more complicated regulations that will impose a quagmire of regulatory uncertainty on large areas of private farmland miles from the nearest navigable water," Duvall continued.

He added that the regulation would threaten progress that has been made on natural resource management and "will make it more difficult for farmers and ranchers to ensure food security" for American families.

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The battle over how to define protected water sources in the U.S. stretches back nearly a decade. During the Obama administration, the EPA issued a rule broadly defining waterways in an effort to reduce water pollution. Then the Trump administration reversed the rule and highlighted which water sources — such as puddles, groundwater, many ditches, farm and stock watering ponds and waste treatment systems — that it wouldn't consider in need of federal protection.

The Biden administration largely restored the pre-Trump regulations.

"The EPA’s latest rule on defining 'waters of the United States' is a statement of federal overreach that ignores states’ authority to regulate intrastate water quality and the Clean Water Act’s statutory mandate for cooperative federalism," Ted McKinney, the president of the National Association of State Departments of Agriculture, said in a statement. 

"In turn, although we recognize EPA’s attempt at clarifying through a roster of exemptions, its rule ignores the voices of nearly all in American agriculture who have long been seeking clarity on this issue, especially regarding the debate over what is and is not a navigable water."

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The National Corn Growers Association (NCGA) has similarly argued that while its members and farmers broadly are in favor of protecting water sources, drainage and water features that are distant from relatively permanent flowing tributaries shouldn't be subject to the regulations.

"We are disappointed that EPA moved ahead with its final rule when the Supreme Court will soon render a decision on this matter," NCGA President Tom Haag said in a statement shared with FOX Business. "The Court’s ruling could negate major elements of this WOTUS rule and will create even more uncertainty for farmers."

"As farmers, we are the ones who will feel the impact of this rule," he continued. "Yet, it appears that our comments fell on deaf ears."

The group also noted that the EPA decided to issue its rule ahead of a key Supreme Court case related to the issue.

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"The National Association of Wheat Growers is deeply concerned that the EPA and U.S. Army Corps rushed to get this revised definition out prior to the end of the year instead of waiting for the decision in the Sackett case before the Supreme Court," Chandler Goule, the CEO of the National Association of Wheat Growers, added. 

"While we continue reviewing the final rule, since the rulemaking process was announced last year, NAWG has stressed that farmers need clarity regarding jurisdiction, recognize important agricultural water features, and more long-term certainty from the courts and administrations," Goule said.

FOX Business reporter Greg Wehner contributed to this report.