There should be a system to detect how deep you are in a body of water, and the player should become more buoyant (harder to swim down, easier to swim up) with increasing pressure. Water already makes players freeze faster, so there should also be a danger of temperature shock when entering a really cold body of water from a warm location. I like the idea of having various stinging cnidarians in coral reefs or at least just a few types of jellyfish. Most importantly of all, the players lungs should explode when ascending from deep waters too quickly.
