The Australian international has scored just once in ten outings for the Teessiders so far this campaign but after again coming close in the 1-1 draw with Millwall on the weekend, Mowbray feels that things are about to turn for the ex-Celtic star.
"Scott hit the woodwork and his follow up rifled against the goalkeeper," Mowbray told the club's official website. "He struck it well enough but another day you mishit it and it goes in.
"I'm sure every striker's been through periods in their career when things haven't gone for them.
"He has to keep going and keep working hard - nobody can ever deny that Scott McDonald works hard for the team.
"What he brings to the side is all the qualities I ask of my strikers but at the moment it's not quite falling to him in front of goal and he just has to keep going."
He added: "Earlier in the season he was making goals for Marvin (Emnes) and we need him to continue doing that and not to be snatching at things.
"He's scoring regularly in training and he just needs one to go in and I'm sure he'll be off on a roll.
"He's a bit frustrated but he knows his work and effort is appreciated for the team. He's the sort of boy who can get uptight about it and the message to him is just to relax and keep playing."