If water is only 1 or 2 clicks deep, you can simply place death squares on the bottom of your water room, and Lara will die on contact if she falls or jumps in. However, if your water is 3 clicks or deeper, this will not work because Lara will start swimming if she falls in. To create death pools 3 clicks or deeper, this is how you do it.
1. Join your rooms, then use toggle opacity 2 and texture your death water or lava water surface.
2. Go down to the water room and look up to the room above; then highlight the area you want to be death.
3. Now hit the death square and apply it to the underside of the room portal.
This won't work if you apply it to the floor of the room above, you must apply it to the ceiling of the room below. If you have done it correctly, your water room ceiling will look like this.