The Senate voted 59-40 on Thursday to confirm the controversial nomination of Gina McCarthyGina McCarthyThe media’s tactics to silence science at Trump’s EPA Overnight Energy: EPA releases ozone findings | Lawmakers come out against Perry grid plan | Kids sue Trump on climate change Congress must come to terms on climate change regulation MORE to lead the Environmental Protection Agency.

GOP Sens. Lamar AlexanderAndrew (Lamar) Lamar AlexanderWeek ahead: Lawmakers near deal on children's health funding Ryan suggests room for bipartisanship on ObamaCare Time to end fiscal year foolishness MORE (Tenn.), Susan CollinsSusan Margaret CollinsDemocrats search for 51st net neutrality vote Overnight Tech: States sue FCC over net neutrality repeal | Senate Dems reach 50 votes on measure to override repeal | Dems press Apple on phone slowdowns, kids' health | New Android malware found Overnight Regulation: Dems claim 50 votes in Senate to block net neutrality repeal | Consumer bureau takes first step to revising payday lending rule | Trump wants to loosen rules on bank loans | Pentagon, FDA to speed up military drug approvals MORE (Maine), Bob CorkerRobert (Bob) Phillips CorkerSenate campaign fundraising reports roll in Congress should take the lead on reworking a successful Iran deal North Korea tensions ease ahead of Winter Olympics MORE (Tenn.), Jeff FlakeJeffrey (Jeff) Lane FlakeMcCain rips Trump for attacks on press Bipartisan group to introduce DACA bill in House Flake's anti-Trump speech will make a lot of noise, but not much sense MORE (Ariz.), Kelly AyotteKelly Ann AyotteLessons from Alabama: GOP, throw out the old playbook The Hill's 12:30 Report Explaining Democratic victories: It’s gun violence, stupid MORE (N.H.) and John McCainJohn Sidney McCainMcCain rips Trump for attacks on press NSA spying program overcomes key Senate hurdle Meghan McCain says her father regrets opposition to MLK Day MORE (Ariz.) voted for McCarthy's confirmation, while Sen. Joe ManchinJoseph (Joe) ManchinMcConnell to Dems: Don't hold government 'hostage' over DACA Lawmakers see shutdown’s odds rising Senate campaign fundraising reports roll in 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 VitterWhere is due process in all the sexual harassment allegations? Not the Senate's job to second-guess Alabama voters The Senate 'ethics' committee is a black hole where allegations die 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 BoxerDems face hard choice for State of the Union response Billionaire Steyer to push for Dem House push Billionaire Steyer announces million for Dem House push 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.