This effect was originally designed by Ben Roffelson. By combining the Sector-Over-Sector and Submergible Water effects, you can create submergible water which seems to have a sector directly below it. The concept is simple, but explaining it is difficult.
Create a room with an above-water sector. Create a hallway attached to the room as shown in the image. Make the end of the hallway cross slightly through the room without sharing any vertices with it. Tag the above-water sector [0,1], and place an S[Channel,7] within it.
Use Right Alt to encapsulate only the above-water sector. It will flash green when highlighted. Use Insert to copy the above-water sector. Now use the Left Mouse Button to temporarily drag the copied sector somewhere else on the map. This new sector will be the below-water sector. Change its tag from [0,1] to [0,2].
The below-water sector's ceiling must be physically lowered to match the true water height (for realism). Texture the ceiling as water, and lower it exactly to the floor. Then you can lower the floor to the desired pool depth.
Attach a small 'window' sector to the side of the below-water sector. It should equal the width of the end of the hallway that was previously constructed. Split the small sector in half. Mask the middle wall of the small sector and change it to an unbreakable window (#504). Make it as transparent as you wish, and give it a palette value of 1 (blue). As you may already have guessed, this sector is eventually going to be attached to the end of the hallway.
Turn grid locking off (with L). Now use Right Shift to encapsulate the entire below-water setup. Drag it as close as possible to the above-water sector without actually touching it. Absolutely none of the vertices can be allowed to connect. In the image, the two sectors are almost overlapped.
Turn grid locking back on (with L). Move the two vertices at the end of the window sector onto their nearest respective grid points (in other words, get them back on the grid). Now connect the end of the hallway with the window sector.
Slope the hallway's floors as if they were stairs. The hallway must travel deep enough for the player to view through the window. In the game, you can submerge under the water and look into the hallway. Then you can surface, walk down the hallway, and see into the water.
