Liner showing problem on large boulders

I am currently building a pond (still digging). I have large boulders that
go 2 ft below water and come 4 ft out of the water. Theyre about 10 ton or
so.
I would like to have the liner below the water line and glue it or silicone
it to the large boulders making it waterproof. I really dont want to show
the liner above the water and stacking stones on the liner and boulder would
be very difficult since it's almost vertical.
Has anyone come across this dilemma?? I see many pond pictures on the
internet with similar setups but they dont tell how the liner is hidden.