You can achieve this by scripting. Place a trigger zone where you want and set as its main script this
;Artificial Intelligence Script
;Header
desc = set water
;Triggers
:state=0:water=1,waterfogdist=500,waterred=210,watergreen=230,waterheightofzone=0,state=1
;End of Script
...where waterfogdist= is used to define the underwater fog distance; waterred= ,watergreen= ,waterblue= , are used to set the water color; waterheightofzone= , is used to set the water height (not sure for this last one

). Just experiment with these commands until you find what you want

And if you need help just ask again
(Well, if you're using FPS Creator X10, I think that the commands will be different, but I don't know them since I'm using the X9..)