Rules: Swimming Dragons

If a dragon has a swim speed, it can swim on the surface or below it without difficulty. It moves through water at the listed speed without making Swim checks. It has a +8 racial bonus on any Swim check to perform some special action or avoid a hazard. It can always can choose to take 10 on a Swim check, even if distracted or endangered. It can use the run action while swimming, provided it swims in a straight line.
A dragon that does not have a swim speed still can swim, but it must make Swim checks to move, and is subject to all the rules governing swimming, including taking nonlethal damage from fatigue when it swims for extended periods (see the Swim skill description, page 84 of the Player’s Handbook).
A dragon swimming underwater must hold its breath unless it has the water breathing ability. A dragon with the water breathing ability can do anything in the water that it can do out of the water, including using its breath weapon.
A dragon holding its breath underwater must obey all the normal rules for doing so. Most dragons can hold their breathes without difficulty for quite long periods, thanks to their impressive Constitution scores. A dragon holding its breath can use its breath weapon underwater. If the breath weapon uses fire, the dragon must succeed on a DC 20 Spellcraft check to make it function properly. If the check fails, the fiery breath merely creates a few harmless bubbles of steam. No matter what kind of breath the dragon used, it stops holding its breath when it uses its breath weapon and begins to drown.