While I was doing my long post, you were doing your pictures. Very nice setup there. Could you move some of the rocks under the drops of the waterfall to get some extra filtration there? I bet you can rig something up if you think about it. I agree with Reddad. I bet you are stil experiencing a bit of runoff. When you get your plantings in around it, you won't notice the liner any longer. I know, right after all that work, you want it to be perfect, not see the liner and have clear water. Been there, done that 6 or so years ago. Now I can't find the edges of the liner, the plantings have taken over so much. It is time for me to tear it all out and replant because they are going all over the place, taking over the world.
When you are ready to plant and now is a good time, send out the word here and usually there is somebody tearing something out and will sell, or send for postage, starts of various plantings. That's how I got all my marginals, mostly for free. Check on the sub forum on the plant exchange.