Just a quick map to show a good way to incoperate a flood into your map. When you press either red button, the grating in the corner closes, and the water rises. Press again to open grate, and allow water to drain away. ...Exciting!! lol.
PS. sorry for the lack of VM, but didn't have time or energy and its only an example map
bangs head against wall
---NOW WITH SELF-ADVERTISING!!!!---
With an animated texture and playing with the fx settings, you might be able to make it look like flowing water as well.