The Slovak international arrived in the summer in a £1.4million deal and has done well when given an opportunity.
But he has been unable to dislodge Paul Robinson at left-back and has been left frustrated and kicking his heels on the sidelines.
Now Mowbray concedes it may be hard to keep the 26-year-old at The Hawthorns.
"Marek is turning out to be a very good professional but he is frustrated and wants to play," Mowbray told the Birmingham Mail.
"He came here to play and has found himself out of the team, and yet he gets his head down and gets on with it and I think he understands that this is professional football.
"At the same time, I have shown in the past with unhappy footballers that if they want to leave I am more than happy to try to facilitate that for them.
"We'll see in the summer how Marek feels about the situation.
"You can't speculate what will happen to Marek but if he's not happy in the summer then I am more than happy to discuss his future with him and his advisers.
"If he needs to get away to play football we will try to make it happen as long as it isn't a detrimental business deal for the club and that he can be replaced."