Wednesday's loss against AFC Bournemouth saw Rovers fall some nine points behind the play-off places, leaving the side with an uphill task of reaching the top six.
But with plenty of games remaining, the manager remains adamant that the season is far from over.
Speaking to Radio Rovers, Bowyer said: "We are going to have to stay calm, we've been in this situation before where it is very easy to jump on the bandwagon and be very negative, but we are not going to do that.
"We are going to continue to fight and that starts at Huddersfield on Saturday.
"We've just got to keep filling them with encouragement and work our way through it. There is nobody who is going to come in and give us a magic wand or anything like that, it is just going to come from sheer hard work and that is what we are going to have to do.
"We had got ourselves into a good position but the last three games haven't been good enough, simple as that.
"The season isn't over, there are 12 games left, we are going to have to have a good go.
"I totally understand the fans frustration because their frustration is matched by ourselves. No-one is happy with it because we had got ourselves into a good position.
"We've got to keep going and to keep looking to ourselves to improve."
Rovers are next in action against Huddersfield Town this Saturday. Tickets are currently on open sale, priced at £25 Adults, £15 Seniors, £10 Under-18s and £5 for Under-8s. Supporters should note that whilst Huddersfield will be selling on the day of the game, there will be no Under-8 sales.