I have river rock on the bottom of my pond. A few years ago I got tired of repotting my lilies each spring, decided to pull them all out of the pots, put them on the bottom and place a large rock on top of them. They are all rooted in and bloom just fine. I have all hardys; pink, yellow, white and red. They have wandered about the pond and mingled, I love this look. The only plant I have potted is my lotus.
This works for me. I know a lot of people don't like rocked ponds, but I do. Each spring before everything greens up, we take a large pump and suck the gunk off the bottom. My pond is about 7,500 gallons.