Don't forget that you'll take double your armor check penalty while swimming. So taking 10 may not be good enough.
If the PCs accept a -10 on their swim check, they can move at their speed as a full round action (CAdv).
You could add in rooms that have air pockets for them to breath in. Place them far enough apart that the PCs need to be smart about their turns or make it so that after the PCs breath there isn't any more air. Because of .. um .. CO2?
You also could put a bottle of air or a breath mask (check the Desmodu entry in MM2) somewhere in the maze, perhaps guarded by a monster. Force the PCs to buddy breath and defend their air source from monsters.
Drowning is pretty rough. Once a PC starts to flounder there's little that you can do for them.
One other thing to consider, can the PCs see underwater? I am picturing this as something similar to exploring an underwater cave so there won't be any natural light too.