The Rovers full back sustained ankle ligament damage during the second half of Saturday's 1-1 draw with Leicester City. Having to be stretchered off the pitch.
Henley becomes the eighth Rovers player to suffer an ankle injury this season, with DJ Campbell, Dickson Etuhu, Markus Olsson, Corry Evans, Ben Marshall, Tom Cairney and Jason Lowe all sidelined with similar injuries during the campaign.
"Unfortunately that might be Adam's season finished," revealed the manager. "Which is a crying shame for the lad and us.
"He's fallen victim to the injury on Saturday that he picked up so that might be him for the season so we are disappointed with that.
"He got his ankle caught as he went to defend the cross against Schlupp and he's gone right over on it and the diagnosis at the moment is that the season might be finished before he is back playing."
Henley's injury means Todd Kane could return to the starting eleven, with Bowyer hoping the defender grasps his opportunity.
The on-loan Chelsea man was a regular at right back at the beginning of the season, but since the beginning of December has had limited opportunities.
"It is now a chance for Todd to cement that position and show that he is a good player," said Bowyer
"In terms of cover we've also got the very versatile Jason Lowe who I think has played in every position for Blackburn Rovers bar in goal and up front."
Tom Cairney is back training but isn't considered for Tuesday's match against Watford, whilst the manager wouldn't be drawn on whether Jason Lowe or Grant Hanley could return.
"One of them has a chance, so we'll just have to wait and see which one that is," added the manager.
"So we'll just have to keep our cards close to our chest, after training you always have to make sure that they recover and there's no reaction so we'll do that.
"Tom has joined in with training with the whole group, so he'll stay and have a full week's training and then on Saturday he should be looking at that."
Tickets for Tuesday's match against Watford will go off sale at Ewood Park at 12 noon. After that tickets will be available from Vicarage Road from 6.30pm on the night of the match.
Prices are £26.00 Adults, £15.00 Seniors over 65 / Students aged 24-20 with valid NUS Card / 16-19 year olds and £10.00 Under 16’s.