Here's an idea:
1. place the water decals in the place you want, or semi-transparent blue entities with no collision if you really want to.
2. Make a simple transparent entity that will be on the surface of the water.
3. Make a static entity with no collision and place that at the bottom of the water.
4. Use a script to associate the player with that entity and have it slowly move it down to give the appearance of floating, also add sound effects at this point if you want.
5. When the entity the player is standing on reaches the bottom of the water, start a script with the condition ANYWITHIN=X in it. The entity the player is standing on should detect the static one that was placed at the bottom of the water. When that condition is met, have a scancodekeypressed=X action that will start the entity rising again. Note here that if you have the W key set as the button to rise then it won't work as it is already coded as the forward action. If you have a version 1.04 of FPS Creator (thats the one I have anyway), it has the action USEARROWKEYS=X in it. If X=0 then you will be able to use the W key as the button to rise through the water, but just remember to enable the arrowkeys again afterwards so the player can walk
.
I'll try and code the script and put it here since this is an idea of mine that might actually work
.
Hope it helps a bit.
so what's the job?