[Sgtmonkeynads]

Technically you would not need to animate it.
Once a compartment is flooding beyond control, the Captain would move to another compartment.
So...in the game we would never see the crew " up to their chest " in the flooded compartment.

Now, lets say the forward torpedo room is flooding and can not be saved what so ever. The door would automatically shut and would seal that compartment off. The flooding could be represented as water squirting out of the seal around the door, and by shouting from the sealed off compartment. If the repair team inside the flooded compartment fixed things and stoped the leak, the door would open( after the time it takes to pump out all the water ) revealing the normal flooded floor we all see. If they don't we all sink.

This would force the captain to stay away from flooding rooms in fear of being traped on the wrong side of a door...if I were in the rear torpedoroom and the engine room took major damage, the door between the engine room and forward torpedo room would close, and i could not get to the control room ( untill it was fixed, if it were fixed ) or if the conning tower was damaged, we could not get out of the sub. That brings up the issue of emergency hatches being made operatable.

I don't know how to do this, but I am sure it could be done.
If it added anything to the game, it would atleast add the element of fear. Fear of being caught away from the comand room, not being able to issue orders, or being trapped in a sub about to suffocate, even tough your surfaced.