As of v735, the underwater scripts will feature drowning.

• Once a character goes underwater, they will be able to hold their breath for a number of rounds equal to twice their Constitution score.
• You will receive a message indicating exactly how much time your character can hold their breath for.
• The amount of time you can hold your breath can be increased with potions, items, and the Sea Caves domain power.
• After this period of time, you will begin drowning, and rolling Fort saves versus increasing DCs, starting at DC 20.
• Whenever one of these Fort saves is failed, you will take d12 points of drowning damage.

Also, note that going underwater wearing heavy armor, with a heavy shield and a heavy weapon will now decrease your speed significantly.

This should facilitate the addition of several new fun underwater areas. :)

Enjoy!