The Senate voted 59-40 on Thursday to confirm the controversial nomination of Gina McCarthyGina McCarthyTrump plans to roll back environmental rule everyone agrees on EPA chief to visit Colorado mine spill site In the fight between Rick Perry and climate scientists, Perry is winning MORE to lead the Environmental Protection Agency.

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“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 VitterYou're fired! Why it's time to ditch the Fed's community banker seat Overnight Energy: Trump set to propose sharp cuts to EPA, energy spending Former La. official tapped as lead offshore drilling regulator 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 BoxerTrump riles Dems with pick for powerful EPA job Pelosi's chief of staff stepping down Time is now to address infrastructure needs 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.