Bobby is right, you can mask your lake easily by a painted shader area. I've made you a little sample. And the rock populations can be distributed using the height restrictions in the distribution shader. Beware that in the preview you only see the cut-off lake in textured preview mode, as shown.
The default shader is used to set opacity for the lakes, only upper one for now, be sure to turn the color to black, so only the painted white area will be water. If you want to check out the painted shader, there's a button on top of the preview, where you can paint.
I used planes for lakes, but you have to uncheck shadows if you do.
I hope this helps.