Nichols' technique of shooting through glass represents something similar to his use of water: it's his way of describing Benjamin's relationship with the world. Ben is always looking through glass: he stares into his fish tank; he looks up at his father through the mask of his scuba suit; he stares at Mrs. Robinson through the glass door of the hotel phone booth; he stares at the TV as Mrs. Robinson gets dressed and leaves the hotel room after sex; he watches helplessly behind the window in the church as Elaine marries another guy.

He's not locked up in some dark room, either. The point is that he can see the world, he's aware of it…but he feels separate from it. He's on the outside looking in at experiences he doesn't know how to feel about. He's cut off from his feelings.

When he comes out from behind the glass partition in church balcony and charges into the church, we know it's an emotional breakthrough.