By the same token, a future president who wanted to direct the E.P.A. to cut emissions more aggressively in order to tackle climate change could face tougher scrutiny from the court.

The Trump administration is also crafting a proposal to weaken Obama-era emissions standards for cars and light trucks that, in one draft version, would rescind California’s authority to set its own stricter vehicle standards. California has threatened to challenge this move in court, but the state’s chances of prevailing now look somewhat murkier.

The shift at the court could also have broad implications for federal efforts to regulate water pollution. In a sprawling 2006 case, Rapanos v. United States, the court split over how the Clean Water Act, which imposes pollution limits in large bodies of water like the Chesapeake Bay, should extend to smaller rivers, streams and wetlands.

The court’s four conservative justices at the time — led by Antonin Scalia, who died in 2016 — argued for a narrow interpretation of the law that limited its reach. The court’s four liberals argued for much broader wetlands protections. Justice Kennedy wrote a separate opinion that ended up in the middle, establishing an elaborate test to determine which bodies of water could be regulated.

In 2015, the Obama administration published a new rule on water pollution, known as the Waters of the United States, that attempted to follow Justice Kennedy’s guidance. But after farmers and private landowners complained that the rule was overly invasive, Mr. Trump asked Mr. Pruitt last year to replace this rule with a much narrower regulation that followed Justice Scalia’s opinion. Mr. Pruitt’s rollback effort could now have a better chance of success if it goes before the Supreme Court.

Justice Kennedy’s retirement could also affect what types of environmental cases and questions get argued before the court.

“You can imagine the Scott Pruitts of the world feeling emboldened and saying, ‘Let’s adopt a more aggressive stance on deregulation and take our chances before the Supreme Court,’” said Jody Freeman, a law professor at Harvard who was the counselor for energy and climate change in the Obama White House. “By the same token, you also might see environmental advocates try to keep cases away from the court if they think they’ll get a worse decision there.”