The Senate on Wednesday voted down an amendment from Sen. Tom Cotton (R-Ark.) that would attempt to block future funds from being used to purchase heavy water from Iran. Here he appears at a Capitol Hill hearing in January. (Alex Brandon/AP)

The Senate on Wednesday rejected a Republican amendment that had renewed tensions over the Iran nuclear deal and threatened to derail chamber leaders’ efforts to pass spending bills this year.

Democrats were blocking consideration of the annual energy and water appropriations bill to protest Sen. Tom Cotton’s (R-Ark.) proposal to prevent the United States from using federal funds to purchase heavy water, which is used in some nuclear fuel reactors, from Iran. The Obama administration made clear it considered the proposal a “poison pill” that would cause the president to veto the bill.

To get around the standoff, Republican leaders scheduled a vote on Cotton’s amendment but set a threshold of 60 votes for it to be adopted. The vote was 57 to 42. The Senate soon after voted 97 to 2 to limit debate and the bill could pass as soon as Wednesday.

Key to ending the impasse was the decision by Sen. Lamar Alexander (R-Tenn.), who heads the Energy and Water Appropriations subcommittee that wrote the bill, to oppose the amendment.

Alexander, warning of potentially “dangerous consequences,” argued that it was better for the United States to have the ability to purchase the heavy water from Iran than to allow it to go to another country.

“The idea of letting it go on the international market and perhaps find its way to countries building nuclear weapons is something I can’t support, so I will be voting no,” Alexander said Wednesday. Only two Republicans opposed the amendment: Alexander and Sen. Rand Paul (R-Ky.).

The vote also exposed some of the continuing tensions among Democrats over the Iran deal, with five Democratic senators voting in favor of Cotton’s proposal.  But two leading Democratic opponents of the nuclear deal — Sens. Ben Cardin (D-Md.) and Charles E. Schumer (D-N.Y.) — stuck with the White House and voted against the amendment.

Cotton announced he would withdraw his proposal after the vote, saying he is “gratified that a large bipartisan majority of the Senate agrees that we should not use U.S. taxpayer dollars to subsidize the program” and noting the importance of having “the Senate on record on this very important issue.”

Tehran is allowed to sell a limited amount of heavy water under the terms of the nuclear pact it signed last year. Last month, the Obama administration announced it would buy 32 metric tons of heavy water from Iran in an $8.6 million deal, a move that stirred controversy.

The resolution of the fight over the Cotton amendment will, for now, allow Senate leaders to continue bringing fiscal 2017 spending bills to the floor — a top priority for Senate Majority Leader Mitch McConnell (R-Ky.) that has the support of his Democratic counterpart Harry M. Reid (D-Nev.).

Democrats have warned that their support for moving appropriations bills is contingent on them not becoming magnets for divisive policy proposals.

Sen. Dianne Feinstein (D-Calif.), the top Democrat on Alexander’s subcommittee, pointed to the vote as proof that “keeping poison pills off of appropriation bills” is key to the Senate working together on spending issues.