What sealant

With our new pond I am creating a smaller header pond with a waterfall into the lower pond via an overhanging piece of stone.

How would you seal between the stone and the liner in the smaller pond?

 

I wouldn't use any seal.
I'd run the liner up under the stone as far as possible and lap it under the header pool.

If thats not possible, use a separate piece of liner to create a gully and place the stone on top of it.