I don't know whether it's the water texture that I'm using, the fact that it's tied to an entity, or that I'm having some sort of graphical issue, but when I tie a water brush to a func_water_analog, there is no underwater fog and I can't see through to the bottom, or through the top of it, like there's a completely opaque layer on top.
It's most likely a special water texture that I am in need of. I'm sure it's not the fact that it's tied to an entity because Valve used this entity and you could see through it. And I'm more than certain that it's not a graphical bug as I have the latest in my graphics card drivers, nor did the problem occur in any of Valve's maps.
Any ideas?
EDIT:
I fixed the problem. After poking about a bit in the textures browser, I found a water texture named "nature_water_movingplane."
As you'd probably guess, it works now
Although, I'm still wondering: How would I get the underwater fog that Valve's map had? No visible fog is there by default.