My system is similar to what you are thinking about, though a bit shallower.
Main pond: about 6' x 10', shelved sides. The deepest is in the middle, perhaps 30".
I used 1" PVC to plumb the water fall. USE LARGER PIPE! Mine is about 20' long and about 3' above the pond.
The upper falls is red lava boulders with some colored concrete to make them look like all one rock and allow the pipe to stick out just a tiny bit. This water falls into a 45 gallon pre-formed pond that is pretty close to a rectangle in shape. (Easy to camouflage with rocks). There is no soil on one side, and it sags. This is fine, this is where the waterfall is. About a foot high.
This water falls into the top of a stream. The excavation is 8' x 20', a large rectangle. Line the whole thing with pond liner. Then fill the sides with peat moss. I used a mesh-like weed mat to keep the peat moss to the sides, and make a winding stream through the middle. Cobbles (rounded river rock up to 8" diameter, but mostly 4"-6") line the pond, and partially fill the floor of the pond. Smaller rounded rock (1"-2" diameter) fills between the cobbles so the weed mat is hidden.
The peat moss planters vary in width, as the stream wanders through the bog. I have all sorts of marginal plants in the peat moss. Japanese Iris, Canna Lily, Calla Lily, Sedge, and others. I have tried cranberries, but they did not live.
At the end of the stream I bunched up the pond liner to hold water in the bog, and create a very small pool above the waterfall. This makes the water level flow better across the rock and out over the main pond. This fall also is about a foot, or a bit more.
I have a concrete block in the water holding up this rock. The fish like to hide in the block. I have not noticed the water getting any harder from the concrete block. It has been in there for many years, now, so any chemical reaction has already happened.
I have Goldfish in there. I have some really large plants in there, too. The pond is pretty much covered with dwarf Myriophyllum, and there are taller plants that I change as often as they die (they live through the winter, here, and live for several years).
If you looked at a cut away of the side you would see:
1) Place for the rocks that make the water fall. This is lined so any water that does not fall free of the rocks will run into the upper pond. This part is pretty much at the soil surface, and in fact the soil is higher here. When we were digging out the bog area we built up the soil in some areas for raised planters. However, in building this we put some concrete blocks in the soil to hold up the boulders.
Dug out for the upper pond. Since this is just heavy duty plastic I was not sure if it would support the boulders that are just about sitting on the edge.
Dug out for the bog. It is about 18" deep. There is a bit of a swale, but not much. The bottom slopes toward the main pond.
Between the pond and the bog is a raised area so the pond liner of the bog and the pond liner of the pond are kept high enough to keep the water in the bog, except for the area of the waterfall.
Main pond is the large part. It started off as a truck bed liner, but I could not keep it sealed, so I dug it out wider and deeper, and added shelves and used Xavan pond liner. It is not worth the extra cost. It is no more flexible than the 40 mil EPDM. Around the edges are flat rocks to hide the liner.