Looking at the pond 1.0 it appears most of the build is more onto of the ground then IN the ground. Think of it this way if you leave the garden hose on while you walk to go shut it off when you get back you find the water pressure has carved into the soil. This is every stream they are the lowest weakest point in the soil and terrain. The water cuts and washes out the weak areas first. Water will ALWAYS take the path of least resistance.
Very rarely is this wash out straight even and consistent. Make your liner much much wider than you think you need. Even if you don't use it for the stream , the liner outside the edging rocks can catch water that splashes from waterfalls and currents. It can also be used to make bog planting areas outside the stream. And help collect rain water easing up on your well or city water.
So all your stream area water should be recessed below the ground level substantially. Let's say your rocks are 12 inches then the stream can have the rocks along the edge be sitting on a shelf where your underlayment liner and underlayment are already set. The shelf at a maximum if it is just one layer. Would be 8 to 10 inches. Why? The Boulder should be higher than the ground level coming up to t he stream so no water run off from the lawn or garden can get into the waterfeature. So a build up along the edge of 2 inches is recommended to deflect this water. Then the liner is tucked up against the rock and some soil . Rocks.gravel. moss wood. Plants and be used to hide this area. But I
You should see next to nothingbof the liner but in Tim we foot traffic will wear this area and could expose the liner.
Making pools at the bottom of the drops or waterfall can give you an area for a light or even a limb or tree stump. Making the stream look like it was always there.