Here's an option.  I created an animation of concentric rings radiating out from a central source.  (I used the "radio waves" filter in AfterEffects, but you could do the same in any number of programs.)  I put this into the bump channel of the shader for this plane along with a fractal noise generator (in add mode).  I spent about 5 minutes throwing this together; if you spent more time animating the concentric rings and also animating the texture of the water (this is just a color and bump), it could look pretty good.

HTH.

 - Dex