Yes, the big home centers should carry or be able to get panelling that can be used for wainscotting and the cap molding for the top also. But you might also check you phone book for locally owned lumber yards and check with them also. They might be more willing to work with you on "what you can get" rather than "this is what we got."
By the way, wainscotting is normally 30 to 36" high and you might want to run some masking tape around your room at various heights to see what height looks best.
Water in the bathroom can be a real problem, so be sure to seal any wood well, including the bottom edge where it meets the floor.