Do you have any extra liner under the rocks?? If not I think you will have to make a change to your pond. If you want the rocks to be in the water the liner needs to extend beyond the rocks and above the water line you desire. What I (and many others) have done too accomplish this is to extent the liner beyond the rocks and above the water line and then use a mix of additional rocks, including smaller rocks and gravel to cover the liner edges.

Forgot to add an additional thing you could try. You could use mortar between the rocks and make sure the mortar extends well beyond the water line. If you were to do this make sure the mortar is completely set up before letting the water level extent to it's level. You could also try rock foam, which is probably the cheapest way to go. I've heard that it is not completely water proof but will do the job in a case like your's.

The liner does extend past the rocks, but there is dirt on top of the liner and in between the rocks. Do I need to remove that dirt and put gravel there instead?

The dirt is probably acting as a wick, so yes it should be removed. Make sure the liner at that point is not slipping down or folded. Packing soil behind the liner to support it is a good idea. Small stones to steady the larger rock is a good idea or you can use Great Stuff to hold the rocks together once you know the leak has stopped.

you should have liner covering the entire waterfall,front to back,side to side.with the sides of the liner cupped up.

also i like to add, you dont need dirt between the rocks, it will just leach into the pond.