First let me say that your pond is going to amazing! I had a similar problem when I decided to build my pond on a slope with ledge and a couple of very large 'immovable" rocks (and also heavy clay soil). Everyone told me to use a liner but I just couldn't figure out a good way to do it.
Here is a photo of everything after it was all dug out (by hand, by me, after two years). The bottom is a solid slab of granite and the pond is about 20' x 10'. I had to go out that far to get it deep enough to overwinter fish
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This is a photo of it all cemented up before it was filled
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I used rebar around the edge and chicken wire on the walls and around the large rocks.
To seal everything I ended up going with Sani-Tred's Perma Flex and Liquid Rubber.
https://sanitred.com/waterproofing-before-after-gallery/ Perma Flex is used in aquariums, pools, ponds and animal enclosures. It goes on very thin but it seals very well (if you can get the surface clean and dry enough). Liquid Rubber is absolute magic. It is made up of a similar chemical mixture to Perma-flex and they will always bond to each other (even years later). You can mix Liquid Rubber up in any thickness and it is VERY useful at filling gaps that need to expand and contract. The second year I had the pond we had a cold winter (I'm in New England) and the granite slab separated from the cement wall at the lowest point. Needless to say, I had to drain the pond in the Spring to fix it and I used a LOT of Liquid Rubber in the gap. 10 years later when I drained the pond to clean it, not only was the Liquid rubber still holding but it still looked like new!
Here is a the pond in aii of it's glory last year. It was built in 2007 and is still going strong!
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There are a lot of products out there. I'm sure you'll find something that will work for you.
Allynn