From my experience they can be underwater for a long time. They usually surface for air every 10 minutes or so, but can hold it a lot longer.
If he's in a water dish then its pretty shallow right? So for him to surface for air it should just require him sticking his head up? Cause that's pretty easy. I wouldn't worry about it, if he wants to surface he will.
Like chinadog said, it is a bit odd that he would just sit in his water bowl? Could you post a pic of the entire setup? That would help.