After watching this a few times you can start to see some of the elements they used. There is a caustics layer of some sort creating the highlights on top of the water. Some textures, some coloring, and some underwater distortion and I think you can make pretty close to what they did.
This piece is basically made up of 3 parts:
I began with what I knew for sure. The top layer was a Caustics generator. I found this in my Apple Motion Library under "Generators".
The next piece of the puzzle is the pool floor. Well the pool floor photo used in the other tutorial had a water mark on it so I didn't want to use that. I simply fabricated mine by combining a Grid and Checkerboard Generator. I gave it some texture using a Noise Filter. But by all means using a photo you took or found online would also work.
The final part was adding my logo. I created the shadow by adding a Drop Shadow on the logo and also duplicating the logo, coloring it black, adding a blur, and plaing underneath for a more realistic look.
Put them all together and you get something like this. It actually looks pretty decent so far. I created some faux lighting with a couple gradients that I Blended using Multiply. A lens flare was also added just to create a little more interest.
The final animation came from me just playing around with effects. The Caustics layer has an Underwater filter on it as does my entire Underwater layer. That alone gave me a pretty convincing effect. Just for a final touch I gave my logo a little bit of randomized movement and I was done. Here is the product.