It would probably be easy for somebody to script, I imagine it would be semi-similar to the creeper game mode. (as in it involves bricks placing themselves)
Create custom 64x64 water bricks at 1, 3, 9, and 18 heights. (brick height, not plate height)
Place these special water bricks throughout the map where you want flooding to occur. This will be the starting flood level.
When the game starts the water level will rise by placing the 1 height water brick every so often, on top of the starting water bricks.
When 3 of the water bricks get stacked they combine to the 3-height brick. (similar to how the trench gamemode combines bricks) and 3 stacks of 3 combine to the 9 height, etc.
The game could simulate water depth too by making the bottom bricks darker blues, and the upper bricks lighter blues.
Add server preferences that include water colors, how often the water rises, and if players are insta-killed when touching the water.