The manager admits that his side weren't at their best last time out as they held Middlesbrough to a goalless draw at the Riverside.
Now as they prepare to face Nigel Adkins' Royals at the Madejski Stadium, Bowyer knows they have to do better.
"That was the worst performance of the season from us," admitted the boss. "We knew that, the supporters knew that and certainly the players knew that.
"But the progress being made, if you like, is that we came away with something from the game.
"That was the pleasing thing, we managed to keep a clean sheet again, and if we come away from Reading on Saturday with another clean sheet then it gives us an excellent chance."
But Bowyer knows that Saturday's match isn't going to be easy. There was little to separate the two sides when they met at Ewood Park back in November as they played out a goalless draw.
Since then, the Royals have picked up in terms of results, none more so than last weekend's 3-1 win over Queens Park Rangers to move into the play-off places.
"They've a top manager and they are a Premiership outfit and they proved that at the weekend by going to QPR and winning so convincingly," added Bowyer.
"They were in the Premier League last season and they haven't made too many changes to their squad.
"We know it is going to be difficult, it was a tough game here at Ewood, so we are expecting that again.
"But we are going into the game full of confidence with a fit and healthy squad and really looking forward to it."
Tickets for the Reading match will go off sale at Ewood at 4pm on Friday. Supporters should note that whilst tickets are available at the Madejski on the day of the game, prices will rise. Full ticket information can be found here