My Pond situation sounds very similar to yours in terms of weak limestone layers and not having the best clay bottom in my pond.
I have had good success with a polymer product that gets drawn into the limestone layers. It can be broadcast incrementally
when the water level is down so as to not need to cover a huge area. Then you can chase the leak up the valley as needed.
Or, if you have the $$$ to throw at it, you can cover a larger area with the product.
Anyway check out my post about it. I have no affiliation with that company, they just did a good job for me and while expensive, it is cheap compared to the other options.
John
