I helped a neighbor lady build a stone and liner pond ten years ago. Yes can cover the liner, though if you might consider some shelf layers to hold rock, sand or gravel on to do so. If you do stone and liner make sure to get a quality liner and be careful setting stones as even tough liners can be torn or ripped easily when setting a several hundred pound stone down onto it.

Here are some pictures of the pond midway through it. I have pictures of end the result but am unable to find where they are, I have looked through 50 folders of pictures to no avail, not sure how I classified them.

[Linked Image from i.imgur.com]
[Linked Image from i.imgur.com]
[Linked Image from i.imgur.com]

I just set the stone in locked together and used fine rock to hold them in place. This pond also has a 45 foot stream with two small pools and a side marsh area fed by a waterfall that drain back into the main pond.