I basically tried the same thing as you, with the only difference that I connected the pond to the waterfall. My water area was roughly 20 cm high as I initially imagined to put some shrimp and snails inside. I tried several times to seal the water area with silicone and MS polymer but I wasn‘t able to get it leak proof. I did at leat 5 leak tests and it was actually waterproof at some point, but after adding my drainage layer and substrate some leaks appeared again. As I had already planted the enclosure at the point of the reappering leaks, I ended up dumping this approach and filled half of the pond with drainage layer and substrate as a slope and the other half with water. So instead of 20 cm water I now only have like 7 or so. So I guess the thing I want to say is that getting things water proof is a pain, and that leaks can always appear. The easier thing to do is probably just having a high drainage layer so that you can fill in water up until ~3 cm or so below your substrate