It sounds kinda terrible, but I can see doing this with a series of maps. The first one is the room with no water in it, but, there's obviously a waterfall (or two) on a wall to suggest what's happening. After a certain period of time, I would virtual-teleport the player to another map that looks very similar to the one they were just in, except that the water level has risen to their knees. Reset the timer, then, when it's done again, virtual-teleport to the room with the water level at (or above?) the player's head. Reset the timer again, and, at the end of that sequence, GAME OVER.
Saying that, there's usually an escape path involved. That's why I'm thinking there would be a timer.