im completely against the idea of damage, it doesn't even make sense mechanicly, wouldn't they recover the damage once they got out of the ocean and could breath again anyhow?

I think one damage per round ended in water would be sufficient. If you want a mechanic you can think of it as if a match were one battle and health represents the general wellbeing of a creature, in which case, the fatigue of treading water for a few hours would be well represented by a loss of health.