If its just the small pebbles you can use silicone. It will hold them in place but it doesn't really make a great adhesive and can be difficult to work with. If I where you I would take rocks (except the biggest ones) off, put silicone down and do it over.
I usually put down great stuff (which can become tacky in 15 minutes), let it dry then shape it. After I am happy with the result I smother the great stuff (working in sections) in silicone and then immediately put my substrate on, firmly pushing it in.
You could also use glue but make sure its non-toxic. Although I believe most brands are after they dry and sit for awhile. Gorilla Glue comes to mind, a member on here used it to build his setup I think.
Good luck
Mitch
