One method is to use an interior tileset that allows slightly elevated walkways next to ground tiles. Make a depression, fill it with placeable water. Adjust the level to suit the flying/swimming phenotype.
Wooden Elven Interiors is one possibily (probably with some reskinning, or placeable floors/walls, to get a more modern feel). Image #4 on that page shows what the elevated walkway looks like.
The features I've mentioned are in CEP and elsewhere.
There may well be much more appropriate tilesets out there. d20 modern, perhaps?
