A Congressional bottleneck that had been going on for years finally got some resolution last week when Senators voted to confirm Gina McCarthy as head of the EPA and Thomas Perez as secretary of Labor.

The confirmation process became embroiled in a controversy over Senate filibuster rules in which Democrats threatened to eliminate the minority party’s ability to block executive branch nominations. After a procedural vote on Wednesday in which Republicans failed to muster enough votes to sustain a filibuster, an agreement was reached that averted a change.

The deal led to the confirmations of McCarthy and McCarthy (who were both nominated for those posts four months ago) as well as that of Richard Cordray, who will head up the the Consumer Financial Protection Bureau after a delay of more than two years.

A dispute over filibuster rules wasn’t the only issue that had delayed the confirmations.

Energy industry split on McCarthy

As head of the EPA’s air and radiation office during President Obama’s first term, McCarthy championed regulations aimed at improving air quality and protecting public health but which also forced the closure of power plants that emitted greenhouse gases linked to climate change. While some in the energy industry – such as American Gas Association president Dave McCurdy – expressed support for McCarthy, the coal industry opposed her confirmation. West Virginia Sen. Joe Manchin, the only Democrat to vote against her and a lawmaker closely associated with the coal industry, said McCarthy “has been responsible for overseeing some of EPA’s most unreasonable and restrictive proposals.”

Perez, meanwhile, was criticized for actions he took with regard to a Minnesota whistleblower case while heading up the Justice Department’s civil rights divison, which some lawmakers characterized as improper involvement.

The votes by the numbers

McCarthy was confirmed in a 59 to 40 Senate vote. Six Republicans voted in favor of her appointment: Lamar Alexander (Tenn.), Kelly Ayotte (N.H.), Susan Collins (Maine), Bob Corker (Tenn.), Jeff Flake (Ariz.) and John McCain (Ariz.).

Perez won confirmation after a 54-46 vote in the Senate that mostly split along party lines. He will replace Hilda Soliz, who resigned as labor secretary in January after serving four years in the post, and will be the only Latino in the Cabinet.

Obama said he looks forward to having McCarthy in his Cabinet “as we work to slow the effects of climate change and leave a cleaner environment for future generations.”

Environmentalists cheered the McCarthy confirmation. Margie Alt of Environment America, called it “the best thing that can happen for our air and our water and our land.” League of Conservation Voters president Gene Karpinski said, “It’s about time.”