The entire effect was done using a single opaque plane (there's nothing actually "in" the water) along with some fake depth and shading below the surface. I then became obsessed with the Koi themselves. Each one uses a single color texture and simple UV distortion, driven by a gradient and a sine wave, to create the swimming motion. Then a very basic "depth" mask was used to make the top of the fish sway back and forth, offset from the bottom of the fish, faking a 3D look.
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This was a fun project to work on and I bet nobody has even noticed it. All of the techniques I used are pretty simple, but they combine together to create a fairly believable fish.
A quick breakdown of how I used simple UV distortion to create the Koi fish (more details on the side bar).