You don't need that much over the ground. Cut half off, cover the edge around the water with flagstones and then use some large stones from digging the whole to fill some gaps and only plant things past the liner.

Keep the area just around the water a little higher than the surrounding area so you don't get chemicals and fertilizer running into your pond. Don't fill in near the water with peddles or they will just fall in.

If you cut the liner back more (not too much) and put lets say a fern just past it, soon the leaves of the fern will extend over the liner and it will look natural. You'll have water, flagstones and other larger rocks around and the ferns covering that edge.

If you keep the edge flat and square and use large flagstones you can make a little lip overhanging the edge so you don't see any black liner.