Thanks for finding and PMing me about it, I don't browse the forums that much lately. Posting here for all to see
Water in Source is largely real-time rendering and actually has no base VTF image, all the VTFs are normal maps and such to define the rendering. This makes it much easier to do what you want here. All we need to do is edit the
$fogcolor attribute in all the necessary VMTs (four of them for the 2fort water, which I used) and rename them so there aren't any conflicts.
I've attached what I fiddled with to get you started, drop them into tf2/materials/water, but feel free to tweak the color yourself to suit your map and what you like. It's in standard RGB format.
If you don't know about it, you can use
mat_reloadmaterial <path (such as water/water_toxicgreen)> to reload a single material while ingame for fast VMT/VTF change checking

Add Immortal's sprite effect ideas and you should be good to go.
Finally, a couple example shots of what it looks like.

