That will mean that the centre-half, who has played in every match for Blues so far this campaign, will miss the final two Championship fixtures of the season.
"He (Dean) has been carrying a groin injury for the last three or four months, it's begun to get worse and affect his training and game management," admitted Monk.
"He has done very well with it he has played through - as a few of them have - but this one has got to the stage where he wants to play in the last two games, but my job is to make the decision and look at the bigger picture.
"The bigger picture is that now we are safe and can plan moving forward we need to make sure he is fresh and ready for next season.
"I wouldn't say he is the happiest, but he understands the reasons why we have had to take him out.
"He will have a small surgery this week and the most important bit he is ready for pre-season. That is the right thing to do and Harlee understands that."
Monk says that Dean's injury was the reason he swapped sides with skipper Michael Morrison in the centre of the Blues defence over recent games.
"A couple of months ago I spoke to Harlee and Morro because it's Harlee's left side and on the left side of defence you are clearing a lot more balls and passing with your left foot.
"That was obviously irritating him a lot more, but we needed to push through.
"I spoke to Morro and that's part of the partnership in the team to have the flexibility to do that."
Monk also said it was testament to Dean's attitude that he played through the pain barrier for so long, for the sake of the team.
"That says a lot about him as a person, it goes for all of them, there are a few with a bit of wear and tear on their bodies, there has been a huge demand physically on them.
"That refers back to their conditioning they can get through - and testament to the work that has been done to allow other muscles to be strong enough to carry him through.
"But it typifies the mentality of Harlee and the team.
"That's what I expect from players, we don't put players on the pitch to put them in any danger but sometimes necessity comes, and you do that if you feel they have the conditioning to get through it."