The Supreme Court on Thursday curtailed the Environmental Protection Agency’s authority to police millions of acres of wetlands, delivering another setback to the agency’s ability to combat pollution.

Writing for five justices, Justice Samuel A. Alito Jr. said that the Clean Water Act does not allow the agency to regulate discharges into wetlands near bodies of water unless they have “a continuous surface connection” to those waters.

The decision was a second major blow to the E.P.A.’s authority and to the power of administrative agencies generally. Last year, the court limited the E.P.A.’s power to address climate change under the Clean Air Act.

Experts in environmental law said the decision would leave many wetlands subject to pollution without penalty, sharply undercutting the E.P.A.’s authority to protect them under the Clean Water Act.

“This is a really disastrous outcome for wetlands, which have become absolutely vital for biodiversity preservation and flood control,” said Patrick Parenteau, a professor at Vermont Law School.

Kevin Minoli, who worked as a senior E.P.A. lawyer from the Clinton through the Trump administrations, overseeing the enforcement of Clean Water Act regulations, said the decision would have enormous practical consequences and estimated that it would affect more than half the nation’s wetlands.

“If you’re in an area with a lot of wetlands, but those wetlands are not directly connected to a continuously flowing water body, then those wetlands are no longer protected by the Clean Water Act,” he said.

The decision was nominally unanimous, with all the justices agreeing that the homeowners who brought the case should not have been subject to the agency’s oversight because the wetlands on their property were not subject to regulation in any event. But there was sharp disagreement about a new test the majority established to determine which wetlands are covered by the law.

Justice Brett M. Kavanaugh, joined by the three liberal justices in a concurring opinion, said the decision would harm the federal government’s ability to address pollution and flooding.

“By narrowing the act’s coverage of wetlands to only adjoining wetlands,” he wrote, “the court’s new test will leave some long-regulated adjacent wetlands no longer covered by the Clean Water Act, with significant repercussions for water quality and flood control throughout the United States.”

In a second concurring opinion, Justice Elena Kagan, referring to the court’s decision in June to curtail the E.P.A.’s ability to restrict power plant emissions, criticized the majority’s interpretation of the law.

“There,” she wrote, “the majority’s non-textualism barred the E.P.A. from addressing climate change by curbing power plant emissions in the most effective way. Here, that method prevents the E.P.A. from keeping our country’s waters clean by regulating adjacent wetlands. The vice in both instances is the same: the court’s appointment of itself as the national decision maker on environmental policy.”

The ruling was also another example of the court’s skepticism of the authority of administrative agencies, said Jonathan H. Adler, a law professor at Case Western Reserve University. “The current court,” he said, “is clearly unwilling to defer to an agency about the scope of that agency’s own power.”

Damien Schiff, a lawyer with the Pacific Legal Foundation, which represents the homeowners in the case, praised the Supreme Court’s decision. “Courts now have a clear measuring stick for fairness and consistency by federal regulators,” he said in a statement. “Today’s ruling is a profound win for property rights and the constitutional separation of powers.”

President Biden expressed dismay with the ruling and said his administration would consider next steps. “It puts our nation’s wetlands — and the rivers, streams, lakes and ponds connected to them — at risk of pollution and destruction, jeopardizing the sources of clean water that millions of American families, farmers and businesses rely on,” he said in a statement.

The case, Sackett v. Environmental Protection Agency, No. 21-454, concerned an Idaho couple, Michael and Chantell Sackett, who sought to build a house on what an appeals court called “a soggy residential lot” near Priest Lake, in the state’s panhandle.

After the couple started preparing the property for construction in 2007 by adding sand gravel and fill, the agency ordered them to stop and return the property to its original state, threatening them with substantial fines. The couple instead sued the agency, and a dispute about whether that lawsuit was premature reached the Supreme Court in an earlier appeal. In 2012, the justices ruled that the suit could proceed.

In a concurring opinion at the time, Justice Alito said the law gave the agency too much power.

“The reach of the Clean Water Act is notoriously unclear,” he wrote. “Any piece of land that is wet at least part of the year is in danger of being classified by E.P.A. employees as wetlands covered by the act, and according to the federal government, if property owners begin to construct a home on a lot that the agency thinks possesses the requisite wetness, the property owners are at the agency’s mercy.”

On Thursday, all nine justices agreed that the agency had gone too far in seeking to regulate the Sacketts’ property.

“I agree with the court’s bottom-line judgment,” Justice Kavanaugh wrote, “that the wetlands on the Sacketts’ property are not covered by the act and are therefore not subject to permitting requirements.”

That suggested that the court could have issued a far more limited ruling, Professor Parenteau said.

“They could have rendered a narrow decision based on the facts of the Sackett case and said, in this case, where a wetland is this small and is not connected to the lake, it should not be subject to federal control.”

Instead, he said, the majority “fashioned a policy for the entire United States based on this one particular set of facts of this property in northern Idaho.”

The two sides on Thursday differed principally on the Clean Water Act’s coverage of wetlands that are “adjacent” to what the law calls “waters of the United States.”

That second term, Justice Alito wrote, “was decidedly not a well-known term of art” and a “frustrating drafting choice.” He said it included “streams, oceans, rivers and lakes.”

But what does it mean for wetlands to be “adjacent” to such bodies of water? Justice Alito wrote the term can mean “contiguous” or “near.” For purposes of the Clean Water Act, he wrote, “wetlands that are separate from traditional navigable waters cannot be considered part of those waters, even if they are located nearby.”

The four justices in the minority took a different view.

“‘Adjacent’ and ‘adjoining’ have distinct meaning,” Justice Kavanaugh wrote, adding that he would have included wetlands that are “separated from a covered water only by a man-made dike or barrier, natural river berm, beach dune, or the like.”

He added: “There is a good reason why Congress covered not only adjoining wetlands but also adjacent wetlands. Because of the movement of water between adjacent wetlands and other waters, pollutants in wetlands often end up in adjacent rivers, lakes and other waters.”

Justice Kagan gave an example of the difference between adjoining and adjacent.

“In ordinary language,” she wrote, “one thing is adjacent to another not only when it is touching, but also when it is nearby. So, for example, one house is adjacent to another even when a stretch of grass and a picket fence separate the two.”

Justice Alito responded, quoting from an earlier decision, that Congress must use “exceedingly clear language if it wishes to significantly alter the balance between federal and state power and the power of the government over private property.”

Justice Kagan wrote that last year’s climate-change decision used similar reasoning, invoking “another clear-statement rule (the so-called major questions doctrine) to diminish another plainly expansive term.”

She added: “Today’s pop-up clear-statement rule is explicable only as a reflexive response to Congress’s enactment of an ambitious scheme of environmental regulation. It is an effort to cabin the anti-pollution actions Congress thought appropriate.”

Lower courts ruled that the Sacketts’ property was a wetland that the agency could regulate, concluding that it qualified under a 2006 Supreme Court decision, Rapanos v. United States, which featured competing tests for deciding that question.

Justice Antonin Scalia, who died in 2016, wrote for four justices in the Rapanos decision that only wetlands with “a continuous surface connection” to “relatively permanent, standing or flowing bodies of water” qualify.

Justice Anthony M. Kennedy, who retired in 2018, said in a concurring opinion that the law required only a “significant nexus” between the wetlands at issue and bodies of waters.

The decision on Thursday rejected that view. “It’s striking,” Professor Adler said, “that no justice sought to preserve the ‘significant nexus’ test Justice Kennedy had articulated in Rapanos.”

Coral Davenport contributed reporting.