The former England under-21 international originally penned a three-and-a-half year a deal at the Macron Stadium in the 2011 January transfer window, arriving from Middlesbrough for an undisclosed fee.
Wheater had been with the Teesside club since the age of 17 and scooped the FA Youth Cup in the 2003/04 season. He later went on to captain the first team and represent Middlesbrough in Europe, before call-ups to the full England set-up followed.
Having also enjoyed previous loan spells with Doncaster Rovers, Wolverhampton Wanderers and Darlington, Wheater left the Riverside Stadium having amassed over 150 appearances and looks set to play a big part in Wanderers' future.
Wheater made 11 appearances for Bolton towards the end of the 2010/11 campaign after completing his move from Middlesbrough. And during his first 345 minutes in a Wanderers shirt, the team did not concede a goal.
In 2011/12 Wheater made 30 appearances for the Whites and popped up with a brace of headers in Bolton’s 2-1 victory over Blackburn at the Macron.