The 25-year-old suffered the injury to the anterior cruciate ligament in his right knee in Sunday's 2-2 draw at home to West Brom.
A club statement issued on Monday read: "Scans have revealed that David Wheater has ruptured his anterior cruciate ligament in his right knee.
"The defender picked up the injury when he landed awkwardly during yesterday's home game against West Bromwich Albion.
"He is expected to be out of action for up to nine months."
The injury means Wheater will miss Wanderers' final game of the season at Stoke next Sunday, which the club need to win if they are to have any chance of staying up.
Owen Coyle's men are two points from safety after blowing a 2-0 lead against the Baggies.
Wheater suffered the injury in the first half at the Reebok Stadium, but played on initially only to be replaced at half-time by Zat Knight.
Bolton also lost Martin Petrov to a knock at the weekend, although Lee Chung-yong returned from a broken leg to make his first appearance of the campaign off the bench.