The Spaniard dislocated his shoulder during Sunday's 1-1 draw at Derby and faces a lengthy spell on the sidelines.
"It hasn't been very good news for us, or for him," Bowyer told the club's official website. "He's going to be out for a while, he's got an operation on Wednesday so we'll just see how it goes from there.
"It is his shoulder, it's popped out and he's done it before unfortunately, so we'll just have to see how he goes with the rehabilitation now.
"The lad is gutted, you saw the level of performance that he showed in the first 30 minutes, he was keen to stamp his mark on the game and I'm sure he'll be sat in that hospital bed wondering what he has done to deserve such bad luck.
"I think we are talking months rather than weeks that is for sure, but hopefully with the medical team that we've got then we can reduce the length of time that has been predicted which is roughly around three months maybe longer."