The Senate voted 59-40 on Thursday to confirm the controversial nomination of Gina McCarthyGina McCarthyOvernight Energy & Environment — Presented by ExxonMobil — Biden administration breaks down climate finance roadmap Obama to attend Glasgow climate summit White House puts together climate finance strategy MORE to lead the Environmental Protection Agency.

GOP Sens. Lamar AlexanderLamar AlexanderMcConnell gets GOP wake-up call The Hill's Morning Report - Presented by Alibaba - Democrats return to disappointment on immigration Authorities link ex-Tennessee governor to killing of Jimmy Hoffa associate MORE (Tenn.), Susan CollinsSusan Margaret CollinsMcConnell gets GOP wake-up call Republicans are today's Dixiecrats Biden's push for unity collides with entrenched partisanship MORE (Maine), Bob CorkerRobert (Bob) Phillips CorkerCheney set to be face of anti-Trump GOP How leaving Afghanistan cancels our post-9/11 use of force The unflappable Liz Cheney: Why Trump Republicans have struggled to crush her  MORE (Tenn.), Jeff FlakeJeffrey (Jeff) Lane FlakeFlake donating unused campaign funds to Arizona nonprofit focused on elections: report Biden nominates former Sen. Tom Udall as New Zealand ambassador Biden to nominate Jane Hartley as UK ambassador: report MORE (Ariz.), Kelly AyotteKelly Ann AyotteBiden likely to tap Robert Califf to return as FDA head Poll: Potential Sununu-Hassan matchup in N.H. a dead heat  Democrats facing tough reelections back bipartisan infrastructure deal MORE (N.H.) and John McCainJohn Sidney McCainProgressives say go big and make life hard for GOP The Biden-Harris train wreck may have its savior: 2024 GOP nominee Donald Trump Kelly raises million in third quarter MORE (Ariz.) voted for McCarthy's confirmation, while Sen. Joe ManchinJoe ManchinPressure grows for breakthrough in Biden agenda talks Climate activists target Manchin Hoyer signals House vote on bill to 'remove' debt limit threat MORE (D-W.Va.) joined most Republicans in voting against her nomination.

“My fight is not with her, it’s with the agency and the president,” Manchin said ahead of the vote. “And the fight will continue until the EPA stops its over-regulatory rampage.”

McCarthy will formally take the reins at the EPA at a time when the Obama administration is stepping up work on controversial greenhouse gas regulations.

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The agency is crafting emissions rules for new power plants.

McCarthy will also oversee development of a more far-reaching plan: carbon rules of the nation’s existing power plants, which create about a third of U.S. greenhouse gas emissions, largely from burning coal.

As a result of the proposed regulations, some Republicans said they wouldn’t support McCarthy, who is currently the agency’s top air quality regulator. 

“This EPA has been a job killer and has slowed economic growth,” Senate Environment and Public Works Committee ranking member David VitterDavid Bruce VitterBiden inaugural committee to refund former senator's donation due to foreign agent status Bottom line Lysol, Charmin keep new consumer brand group lobbyist busy during pandemic MORE (R-La.) said after the Senate voted 69-31 to end debate on her nomination. “She is not an outsider. She’s been at the very heart of many of these matters as head of the EPA’s clean air efforts. … For that reason I will vote against her nomination.”

Vitter said he wanted more transparency from the EPA on its decisionmaking process.

Senate Environment and Public Works Committee Chairwoman Barbara BoxerBarbara Levy BoxerFirst senator formally endorses Bass in LA mayoral bid Bass receives endorsement from EMILY's List Bass gets mayoral endorsement from former California senator MORE (D-Calif.) said shortly before the final vote that having a Senate-confirmed EPA chief to replace acting Administrator Bob Perciasepe will have a big effect. 

“I think it will have an impact on every single thing that happens,” Boxer told reporters in the Capitol. “The first may be, in my opinion, addressing the chemical explosion at West, [Texas] and also moving forward on all sorts of rules dealing with water, drinking water, clean water, also dealing with greenhouse gas emissions, methane, all that."

Democrats pointed out that McCarthy’s work on air quality has saved lives, and that she is a bipartisan choice because she formally worked for then-Gov. Mitt Romney (R-Mass.). She was Romney’s undersecretary of policy at the Massachusetts Executive Office of Environmental Affairs, and deputy secretary of operations for the cross-cutting Office for Commonwealth Development that Romney created, work that included development of policies on smart growth and climate change.

Alexander voted earlier Thursday to advance McCarthy toward final confirmation, and he told reporters he would support her again during the final vote.

"She has worked for five Republican governors, one of whom was the Republican nominee for president of the United States," Alexander said, referring to Romney. "And I don't think it is likely that we are likely to get another nominee by President Obama with better Republican credentials."

Republicans agreed to hold an up-or-down vote on her nomination as part of a deal to avoid Senate rule changes limiting the minority's right to filibuster executive branch nominees.

In May, Republicans on the Senate Environment and Public Works Committee boycotted her confirmation hearing. Democrats criticized Republicans for the boycott and because they submitted more than 1,000 questions for McCarthy to answer.

Boxer said this is the longest time that the EPA had been without a Senate-confirmed administrator since Lisa Jackson stepped down at the beginning of the year.

“The EPA deserves a leader and this woman, Gina McCarthy, deserves a promotion,” Boxer said.