I'll try and illustrate the problem as I see it as best I can. There may be ways around it, and if so hopefully someone who understands the node network much better than I will show it.
Here is a sample node network to get some fake looking water transparency:
When rendered you get:
Now if you want to add some fake stones you are going to get something like this:
This is because what you are editing is the water layer itself, not the surface underneath. You have to remember that anything you have underneath the water layer will not be seen because the water is not transparent in any way. Eventually it should be no problem to build your surface with whatever you want, then put some transparent water on top, but that is not possible yet as far as I am aware.