The centre-back joined a host of ex-Boro Academy players to make moves to Premier League sides when his transfer was completed on Wednesday night.
Although undisclosed, the fee is around the £3m mark and the Boro boss will try to use some of that money to replace the Redcar-born defender.
Rumours surrounding Wheater's future at the club began well before Christmas, as Boro could not offer their former captain the long-term deal he wanted.
And with his contract expiring in the summer, Boro were resigned to losing the stopper now if they were to get any money for him.
Despite the situation regarding his future stretching over a few months, Wheater continued to be one of Boro's most consistent performers, something his former boss feels says a lot about his character.
"He's a player if we could have given him a long-term deal, we would have," the Boro boss said.
"He had six months left on his contract, he wants to play in the Premier League, his family and advisors want him to play in the Premier League and we had to make a decision.
"Either we kept him for the next four months and let him walk away from nothing or we sell him now and get some much needed money back into the club and move on without him.
"We wish him well. As long as I've been here the last ten weeks he overcame the speculation and performed magnificently, which is credit to himself.
"I spoke to Owen Coyle the other night and congratulated him on getting a real good professional and I'm sure he'll do a real good job for them."
Wheater's departure now leaves Mowbray with a rather big hole to fill and admits he has made inquiries for potential replacements.
Seb Hines is an option, after impressing since his return from injury, particularly in the home win over Cardiff last month.
But Mowbray admitted bringing former Boro man Andrew Davies back to the Riverside could be an option.
Davies spent six years at the Riverside before leaving for Southampton and then Stoke City, but he now finds himself surplus to requirements at the Britannia Stadium and has been training back on Teesside for over two months.
Mowbray did rule out a move for Abdoulaye Meite, who he signed when manager at West Brom.
"It's important we find another central defender to try and fill that hole and we will try and do it cost effectively," Mowbray said.
"I think Andrew Davies is a little way off at the moment to being a Boro player, I've had one or two conversations with Stoke City over the last few days and I'm waiting on them getting back to see whether there is anything that can be done on a short term basis.
"He's been here awhile but he's not played for a while so the best option would be to potentially loan Andrew and see how he gets on.
"He has a fabulous personality around the place. He's a talker and natural leader and I'd like to see him out on the field in a competitive game."
Mowbray admitted Wheater's departure might not be the only one this month, but insisted Estonian winger Tarmo Kink would not be leaving.
The Boro boss also confirmed Mido looks set to sign for Egyptian side Zamalek, after the striker failed to turn up to the club's training HQ earlier in the week.
Another situation rumbling on is that of Andrew Taylor, who recently returned from a loan spell at Watford.
Mowbray is keen to keep the 24-year-old but faces a struggle to convince the player to stay, and change positions.
The boss believes Taylor would be better suited to a left-midfield role, but the Hartlepool-born full back has reservations, with Watford guaranteeing him a defensive spot.
"I think it's unlikely that he will leave but his contract situation is very similar to David Wheater's in that it's out in the summer," Mowbray explained.
"The difference is there's another club out there offering a lot of money for him but he is our player and I like him.
"I've had lots of different conversations, and he's unsure where he sees his future and I think the uncertainty at our football club in the fact I'm trying to change his position from a full back into a midfield player.
"He doesn't know whether that is going to be a benefit to his career or not. My argument to him is I think it will be a benefit to his career.
"It's not a financial issue for him it's a footballing decision and I'm trying to convince him I can turn him into a top class left midfield player."
Source: Northern Echo
Source: Northern Echo