Opponents of strip mining won passage of the federal Surface Mining Control and Reclamation Act in 1977. It regulated but did not outlaw surface mining, which was often more economical than deep mining. The act specifically allowed mountaintop removal, but only as an exception when the resulting flat land would be used for development.

Mountaintop removal mining, which had begun in West Virginia in 1967 at Cannelton, became more feasible as huge earth-moving machines were introduced into the rugged Appalachian terrain by the early 1980s. The "Big John" dragline, capable of moving 65 to 75 cubic yards at a scoop, came to the Hobet 21 mine in Boone and Lincoln counties in 1983. Today the largest machinery moves more than 100 cubic yards at a time.

By the mid-1990s, the 1990 Clean Air Act amendments had spurred demand for the low-sulfur, high-Btu coal of West Virginia's southern coalfields. More than 500 feet was being shaved off the tops of mountains and dumped as valley fills. At least 500 miles of streams had been filled, and more than 300 square miles of West Virginia had been surface-mined in some way by 2000. Residents complained that blasting shook homes, and dust from mining and preparation plants covered houses and cars. Runoff from valley fills flooded streams and homes. Some communities were nearly eliminated when mines bought out residents who complained.

In 1998, attorney Joe Lovett of Mountain State Justice in Charleston filed a case in federal district court charging that state and federal laws prohibited dumping the tops of mountains into streams. He also argued that there had been complete disregard for the original congressional intent of using the flattened mountains for commercial development. Patricia Bragg of Pie in Mingo County was the lead plaintiff in the case, known as Bragg v. Robertson. Lovett was joined by co-counsel Patrick McGinley and Suzanne Weise of Morgantown, and James Hecker of Trial Lawyers for Public Justice. They won a major victory in October 1999 when Chief U.S. District Judge Charles H. Haden II ruled that a 100-foot buffer zone prevented waste placement in streams that ran at least part of the year. However, Governor Cecil Underwood, coal companies, and the United Mine Workers of America protested. Haden stayed the decision. In April 2001, the Fourth U.S. Circuit Court of Appeals overturned the decision, stating that the case should be tried in state court.

Though the U.S. Supreme Court declined the Bragg v. Robertson case, Lovett persisted and in May 2002 won another dramatic decision from Judge Haden. In the new case, Kentuckians for the Commonwealth v. Rivenburgh, Haden ruled that the Army Corps of Engineers could not, under Section 404 of the Clean Water Act, allow valley fills in perennial and intermittent streams. He agreed with Lovett's interpretation that fills are waste material and therefore prohibited by Section 404, which only allows waste in streams for development, such as shopping centers. Valley fills are allowed, Haden ruled, only when land flattened by the mountaintop mine will be used for housing or commercial development, as the Surface Mining Control and Reclamation Act intended. This ruling was overturned on appeal. Yet the battle over valley fills continued.

The industry won one round when the Bush administration changed Section 404 in May 2002, making valley fills legal. But opponents halted fills again with a July 2004 victory in federal court. Judge Joseph R. Goodwin, who took over after Judge Haden's death in March 2004, ruled that the Corps of Engineers must stop the routine, seemingly automatic approval of valley fills under Nationwide Permit 21. Now the Corps must thoroughly examine the environmental impact of large fills, perhaps denying some. Yet, despite the stalemate on fills, coalfield observers sensed a shift toward more productive use of mined-over flat lands, closer to the spirit of the 1977 legislation. These observers cited the use of mined land for golf courses, industry, and housing, especially in Mingo County.

Between 2004 and 2010, rulings from various federal regulatory agencies encouraged one side or the other on this volatile issue.

During the presidency of George W. Bush, it appeared that the federal attitude toward the practice was more permissive. Anti-mining activists viewed the election of Barack Obama as producing a president more sympathetic to their cause.

Shortly after taking office, the Obama administration announced it was taking steps to reduce the environmental impacts of mountaintop removal. The Environmental Protection Agency began more rigorous reviews of the valley fill permit applications being considered by the Army Corps of Engineers and announced new guidance for agencies considering water pollution permits.

An EPA administrator recommended that the agency reject the permit for Arch Coal Company's Spruce Mine in Logan County because of concerns over the impact of the enormous operation on the environment. The state's political leaders denounced the move. In October 2010, Governor Joe Manchin ordered the state Department of Environmental Protection to file a lawsuit against the federal EPA and the Corps of Engineers. The National Mining Association also has taken court action to put a halt to the more rigorous reviews. In January 2011, the EPA announced it was revoking the mine’s water permit.

The issue of mountaintop removal became a critical one during the 2010 election in West Virginia. The coal industry donated millions to candidates who opposed more rigorous regulation. In West Virginia, some candidates emphasized their support of coal mining, while others were outspoken in their opposition to the practice of mountaintop removal. In campaigning for the U.S. Senate, Ken Hechler, who was 95 at the time of the election, said he was running on one issue—ending mountaintop removal. Earlier in 2010, Hechler, a former congressman and secretary of state, was among a group of demonstrators who were arrested outside a coal preparation plant in Raleigh County.

From a federal government standpoint, issues involving mountaintop removal have shifted depending on which party is in power. Although President Barack Obama, a Democrat, placed greater scrutiny on the practice, particularly in terms of environmental costs, opponents of mountaintop removal frequently criticized Obama for not doing more. Meanwhile, Republicans and the coal industry campaigned that Obama had declared a “War on Coal.” This public campaign, as well as the shifting political tide of the early 21st century, helped flip West Virginia from a reliably Democratic state to an overwhelmingly Republican one in the 2010s and 2020s. Upon taking office in 2017, Republican President Donald Trump rolled back many Obama-era regulations on the practice and canceled a federal study on mountaintop removal’s health effects. After becoming president in 2021, Democrat Joe Biden pledged to restart the study; however, as of 2024, the study was still on hold, and Biden had not nominated a director for the Office of Surface Mining Reclamation and Enforcement.