Markus Olsson will be assessed this morning to determine the extent of the leg injury sustained in yesterday's draw against Middlesbrough.
The Rovers full back was unable to continue after a strong tackle on Dean Whitehead midway through the first half.
The Swede, who has been in outstanding form this term, tried to play on but eventually limped off.
"We'll assess him more and we'll know more tomorrow," Bowyer told Radio Rovers after the match.
"But initially it doesn't look too great."
The injury to Olsson could be tempered by the possible return to action of fellow full back Tommy Spurr.
The defender has missed the majority of the season with a groin injury but is closing in on a return to full fitness after a successful operation.
Should Spurr come through this week untroubled, he could make the squad for Saturday's FA Cup match against Charlton Athletic at the Valley.
"Hopefully Tommy can have a full week's training," added the Rovers boss. "Then he might get some involvement at Charlton.
"If he can get a full week's training in then that is something that we'll look at."
Tickets for the FA Cup match against Charlton are on open sale for the match priced at £10 for Adults, £5 Concessions. Book online today at www.onerovers.co.uk.