The Senate cleared its annual defense policy bill this week, but the military bill faces a handful of hurdles before it can become law.

The House and Senate will now try to merge their two bills, with both sides pledging to finish up their work next month.

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If they can manage to stick to that timeline, it will mark a sharp contrast from recent years when lawmakers scrambled to finish their work by the end of the year.

Here's a look at some of the biggest challenges lawmakers face.

Guantanamo

The Senate’s version of the bill provides President Obama with a path to close the prison in Guantanamo Bay, Cuba—if Congress signs off on the plan. That puts the Senate bill squarely against its House counterpart.

In the House, lawmakers didn’t include an option for closing the prison, but instead would maintain restrictions on transferring prisoners.

The House bill also adds additional certification requirements, bans detainees from being transferred to “combat zones” and blocks any transfers of prisoners to the United States including for medical purposes.

Sen. John McCain John Sidney McCainMomentum growing among Republicans for Supreme Court vote before Election Day McConnell urges GOP senators to 'keep your powder dry' on Supreme Court vacancy McSally says current Senate should vote on Trump nominee MORE (R-Ariz.) also could face pushback in a conference from fellow Senate Republicans.

Sen. James Inhofe (R-Okla.) had hoped to get the Senate to vote on stripping language allowing the administration to close the prison from the defense bill. He now hopes to take that fight to the conference committee.

“Closing Gitmo will not end any propaganda machine, but instead bringing detainees to the United States will only increase risks for Americans,” he said in a statement. “I intend to fight to remove the Senate language during the conference of the defense bill between the House and the Senate.”

Acquisition Reform

Rep. Mac Thornberry (R-Texas), the chairman of the House Armed Services Committee, is eager to reform the Pentagon’s acquisition rules.

As such, the House defense bill overhauls the Defense Department's process for acquiring weapons and services.

The Senate bill goes further than its House-counterpart, shifting some of the Pentagon’s buying power currently held by Frank Kendall, the department’s undersecretary of defense for acquisition, technology and logistics, to the military services chiefs.

Republicans in the House and Senate might be able to reach a deal.

Thornberry has suggested that he’s open to the Senate’s extra reform efforts, and McCain sounded cautiously optimistic that his plan would survive the conference committee.

“I hope to make an argument that he could agree to, but I can’t guarantee it obviously,” McCain said.

McCain also faces pushback from the White House, which argued that his reforms would seek “to exclude the [defense] secretary and his assistants from certain matters entrusted exclusively to the military departments."

Military Pay and Housing

The House defense bill rejects the Pentagon’s proposed cut to military housing assistance and would raise troop pay by 2.3 percent.

The Senate bill includes just a 1.3 percent pay hike, and has come under fire from the administration for restricting housing stipends when both spouses are in the military.

Both issues are very controversial with military families.

While McCain argued that the Senate’s version of the defense bill “focuses on improving the quality of life" for troops, his proposals have garnered opposition from Military Officers Association of America, which argues that the “Senate's proposals reverse much of the hard work Congress enacted between 2000 and 2010.”

Obama’s veto threat

Obama has threatened to veto both the House and Senate bills.

It’s a familiar threat for lawmakers, but Senate Democrats warn that this year the president means to make good on his promise.

McCain suggested that he’s not confident he would have the votes to overcome a veto.

“You don't know what kind of pressures might be exerted in the case of a veto,” he said, adding that he’s willing to work with the administration to try to reach common ground while the legislation goes through the committee process.

It’s unlikely, however, that lawmakers will remove the administration’s main objection: An extra $38 billion folded into the Overseas Contingency Operations (OCO) fund that isn’t subject to congressionally-mandated spending ceilings.