It might be helpful if someone describes how Marathon's swimming model works:
Being underwater, everything functions identically to how it does when you are above water. Forward/backward/left/right move you about just like they always do. However, you move more slowly, which also includes falling (you fall more slowly), and - the really big important difference - the key which makes you 'run' above water (that is, the one that increases your speed when held, not the one that makes you move forward to begin with) will make you float upwards when you are under water.
So, if you are trying to pass through an underwater door, and you try to "run" though it, you will float upwards. Don't try to run. Just walk through it. (Seriously - in real life, have you ever tried to run underwater, on the bottom of a pool? Even presuming you were skinny or muscular enough to sink instead of float, it's damn hard, and you just push yourself to the surface if you try).
Oh, and the other important difference is that you can change your speed and direction with the movement keys *while* floating up or down, which gives you three axis of linear movement (although your facing/orientation is still limited to the same general plane due to engine limitations).
