I don't have any capx for the example you linked, but it seems like the "water" effect is applied to the water, with decreasing parameters (lerp over time ?), and parameters going up when a rock hits it (depending on the rock's parameter maybe ?)
Well, I tried a little and it started to resemble your link, but it seems quite a lot of understanding of this effect is required to do it well (or a lot of tries at least). Help from someone knowing it more would be welcome :)