Tips on making fluid looping 2D water?

The animated fish are relatively complex because the fins move and the body shape changes. With the right kind of artwork, you could get close using AE's puppet pin tool. You would not animate the position but you would animate the wiggling of the fins and the body shape making sure that the starting and ending frames were identical so you could generate a perfect loop.

The second step would be to pre-compose your animated fish, draw a closed path mask on the Pre-comp that would work as a motion path, set a mask keyframe, and cut it, then set a position keyframe and paste to turn the circular mask path into a motion path. You would then extend the path keyframes so the starting and ending position would match the starting and ending identical fish animation frames. You would then turn on Orient along Path for the fish layer. 

You repeat the same procedure for all of the versions of your animated fish then set up the layers so some fish swim behind the subject and others move in front. 

When all of that is done, as long as the first and last frame of the animation is identical, you can then seamlessly loop the final composition.

If you want to get really fancy you could look up Caustics to create a looking down on a pool effect on top of the whole thing. The key to making the loop work is to make the first and last frames identical, then export a video that is one frame shorter for looping in the web or by nesting the comp in a longer comp and looping playback with Time Remapping and a loopOut() expression.

Nothing to see there along the lines of expressions and given how the fish are "pumping" and changing size it doesn't even look particularly advanced. No offense, but it literally just looks like the usually hacky, unsophisticated use of the Puppet tool with as few pins as possible. the rest is just a question of timing, as always with any type of animation.

Mylenium