Grant Hanley was forced to sit out Saturday's 4-0 thumping at Bolton Wanderers on Saturday, while Matt Kilgallon limped out of that contest with a groin complaint.
With Scott Dann having left Ewood Park for Crystal Palace in January, Rovers suddenly find themselves down to the bare bones at the heart of their back four.
It is hoped that Hanley will be ready to return against Burnley next time out, and that Kilgallon will not be out of action for long, but Bowyer has been left with a serious selection headache.
Taking that into action, the Rovers boss concedes that he has little choice but to explore the loan market for possible additions - with Manchester United's Michael Keane reported to be a top target.
Bowyer said in the Lancashire Telegraph: "We will try and bring in a bit of cover.
"It's been well documented that we're trying to do that, but obviously with Matt limping off there is even more urgency now.
"Matt has a slight groin injury and we'll assess that and we're certainly hoping Grant will be fit, that's for sure. He was close on Saturday."