I agree with John above, that the situation isn't automatically fatal. People survive sinking ships pretty often, of course people die in those situations pretty often too. The player should have a chance. What are his odds, and what might affect his chances? How encumbered is he, heavy armor, Olympic swimmer skill? The details aren't as important in my opinion as the point that player death shouldn't come down to just 'there's no chance, you're dead.' This is where "saves" actually come from. The player has a chance to roll his die to avoid the spell, paralysis, etc.
So he can breathe water, but apparently the danger is from being trapped in the ship for longer than the breathe water. In that case you might say, for each round the character stays inside the ship his swim check is going to take a -4 penalty, and iuf he fails it the character dies. This way the player is aware of the stakes, as Blueluck wrote above, but he also had a way to judge how many rounds he's we willing to search. In that case, I bet he doesn't search long... Also in that case the player has some role in the death, he failed swim checks or whatever saves you guys settled on, but he failed the saves not 'the GM just said the character dies'. That's what makes a death feel arbitrary.
