WASHINGTON—The Senate approved a measure aimed at challenging a new Biden administration clean-water regulation, but it faces an expected White House veto. 

The resolution, which has already passed the House, cleared the Senate Wednesday in a 53-43 vote. It seeks to revoke a Biden administration rule that expanded the definition of waterways subject to federal pollution regulations.

Supporters of the resolution say the Biden rule expanded protections to insignificant bodies of water, such as some seasonal or temporary streams, creating unnecessary regulatory hurdles for farmers, home builders, pipeline projects and others. Critics of the Biden rule think the federal government is overstepping in an area that should be left more to states to decide.

“Mr. President, are you going to listen to the heartland of America, where your overreach in your regulatory environment on the waters is going to penalize so many people?” Sen. Shelley Moore Capito (R., W.Va.), the top Republican on the Environment and Public Works Committee, said this week. 

The administration aimed for the new rule to restore protections in particular for arid Western states such as New Mexico and Arizona. Democrats said the rule strikes a balance between protecting communities from industrial and chemical pollution in waterways, while also giving some flexibility to farmers. 

The Biden rule includes an exception for farming on prior converted cropland, which comprises 53 million acres, Sen. Tom Carper (D., Del.), chairman of the Environment and Public Works Committee, said on the Senate floor Wednesday. 

“The rule protects the nation’s waters, wetlands and provides flexibility for those who need it,” Mr. Carper said. “How private property owners manage their land has the potential to affect us all.”

The White House has already said President Biden would veto the measure, and currently there aren’t enough votes to override him.  

The Biden administration rule, issued in late January, defined which waters would be regulated under the Clean Water Act. It went into effect last week in all but two states; a federal judge blocked it from going into effect in Texas and Idaho.

Under former President Donald Trump, Environmental Protection Agency regulators rescinded an Obama-era rule that expanded federal oversight to protect wildlife and the country’s drinking-water supply from industrial runoff and pollution. The Trump administration said some of the protected areas were dry land. 

According to the Army, whose civil works division handles major waterway development and management projects, the Trump-era EPA rule led to a 25 percentage-point reduction in “determinations of waters that would otherwise be afforded protection.”

Most Democrats had backed Mr. Biden’s rule, saying the Trump regulations had left communities at risk of being exposed to pollution. But some Democrats in conservative-leaning states voted with all Senate Republicans to revoke the Biden rule.

“There’s so many things they’re trying to control,” Sen. Joe Manchin (D., W.Va.) said of the Biden rule, which he voted to revoke. “It’s just an overreaching situation.” 

The measure passed under the Congressional Review Act, which allows the Senate and House of Representatives to overturn regulations completed by the executive branch in the previous 60 legislative days using a fast-track process that requires a simple majority vote.

Farmers have been among the most prominent critics of both the Obama and Biden rules, saying they amount to government overreach on private land. The American Farm Bureau Federation said the Biden rule could interfere with farmers’ ability to plow or build fences near small bodies of water on their land without having to secure permitting or risk fines. 

“The rules just constantly change,” said Don Guinnip, who grows corn and soybeans in Illinois. Mr. Guinnip said his primary concern involves his drainage in his fields, which he worries could be drawn into federal crosshairs. 

Lawmakers, farmers and the court system have long been mired in dispute over the federal government’s reach in deciding which bodies of water fall under the Clean Water Act, which can determine permitting requirements and other responsibilities. 

When Congress passed the Clean Water Act in the early 1970s, lawmakers didn’t define which “waters of the United States” fell under its purview, leaving it up to federal agencies to decide how to implement it.

“There’s been such confusion over the definition of WOTUS really since the inception of the Clean Water Act,” said Courtney Briggs, senior director of government affairs for the American Farm Bureau Federation. 

The Supreme Court is expected to issue a decision soon about how to apply the Clean Water Act to wetlands.