Mr Lamont said he had “reluctantly” come to the view that he could not support the deal as it stands. In the Commons last week, he told MPs that he had "lost sleep" over his decision.
In a statement, the Berwickshire, Roxburgh and Selkirk MP said: “I have never doubted the Prime Minister’s commitment to deliver the best for this country... she has had an almost impossible job to do.”
“There are clearly significant risks associated with this Withdrawal Agreement, including the potential that fishing could be traded away and the possibility that we will be locked in to the backstop arrangement.
“This deal could mean that we retain some of the worst things about EU membership without being able to take advantage of the opportunities of Brexit. The UK could end up in an uncomfortable half-way house - having to follow EU rules without any influence or say over them.
“I have come to the conclusion that on balance, these are not risks I am prepared to take."
Mr Lamont was seen as a loyal backbencher, and served as a whip in the Scottish Parliament before being elected to Westminster. He also helped run Ruth Davidson's leadership campaign.
“While there is little consensus about what should happen next, the clear message that I have received from my constituents was that this agreement does not satisfy many.”