You could use the Sculpt Geometry tool or the soft modification tool.

You could also start off with a much lower dense mesh for the ground and then push and pull verts.

Another option would be to use curves and loft tool.

edit: Looking at the reference picture and your bottom screen shot, the reference picture is at an angle (ie. the camera is above the ground, not level with it). In the bottom screenshot, your camera is level with the ground plane. Are you sure that the stones are on uneven ground. Kinda looks like the stones should be on level ground but I've never been there so I'm not 100% sure on this. Maybe look for some more reference pictures on the net to see if it's the stones that need adjusting and not the ground...although the ground is probably not completely flat.