The midfielder caught his studs in the turf in a challenge with Derby's Jeff Hendrick midway through the first half, and after lengthy treatment was eventually stretchered off with suspected ankle ligament damage.
"Ben Marshall has got a bad looking injury," revealed Bowyer on Radio Rovers.
"He has gone for a scan straight away so we'll know more on that one after the weekend.
"I've seen the challenge and the medical team have had a look at him and given their assessment on him.
"So we'll let it settle down overnight and then we'll pick it up after that, but it is a disappointment for the lad because he has been playing out of his skin.
"We think it is ankle ligaments, we've had a few of them this year. Just when you think you are getting everybody back we have this.
"It will give someone else an opportunity and that is what we will focus on starting tomorrow."