I just ran my group through the underwater encounters in Whispering Cairn. The session went ok, but in retrospect I could have handled it a little better. My advice to others running the encounter for the first time:
1) Bring a roll of string. Apparently, the whole tie-a-rope-to-the-fighter and have them swim on ahead is a pretty common response. I had a problem with the players (as opposed to the characters) knowing when to pull back unconscious party members. What i should have done was run a string under a door, and then send all the non swimmers into the next room. A knock could indicate when a round has elapsed, since it takes a lot longer than six seconds to role play a round. You could pull the string to simulate the motion of the characters and let the players decide if the character is unconscious or paralyzed or whatever. Remember how long the rope is. Remember if the players wrap the rope around a column.
2) Bring a flashlight. Always more dramatic to turn off the lights when the players get plunged into darkness.
3) Establish how fast the players can pull back a player if they're all tugging. I said 15 feet/round...what to you guys think?
4) (Hardest for me) Be psychologically prepared to kill off a player. This is dangerous stuff, and it's entirely reasonable that a player die. Particularly if they ignored the hints you dropped about buying potions of water breathing from the Benazel the Alchemist. (Scroll of water breathing from Allustan would be better but you wouldn't want to give everything away now would you?). Particularly if they're being used as bait. I hate to do it, but if you follow the rules it's the players killing themselves now, isn't it?
Good Luck! Hope this helps other DMs!