Not an expert, but several reports on Pond Boss of leaks in the dam after it was breached and subsequently repaired. I believe it is very difficult to seal the "repairs" against the old core trench.
You said, "... rebuilt the gap they cut to drain it, rebuilt the inside of the dam and cored it."
Did they core the whole dam, or just the gap that they had cut?
How were they compacting the repaired core, especially at the top where it was steep? Were they wetting the clay while compacting?
I do like it that your pond only started leaking with the last 3-5 feet of water in the pond. That PROBABLY means your leak is shallow. However, it could still be a bottom leak. Sometimes the extra bit of hydrostatic pressure due to a higher water elevation can push water through tight material that otherwise does not leak.
If it is a shallow leak, then it is likely due to the breach repairs. However, there could be other causes. Do you currently have muskrats at the pond? Did the old pond have muskrat damages. Those b*astards can burrow back a long way into a dam. Water could be entering an old burrow and then working downwards beyond the core trench to exit at the toe of the dam. Likewise, some of the old tree roots in the dam could still be rotting out. They could create a water leak pathway similar to a muskrat burrow. Either would present as a shallow leak.
Did the first bentonite treatment have a noticeable effect on the leak rate? Will you be able to tell if your second (larger) treatment does any good?
If the leak is not affecting your water level much, you might just leave it as is. Most leaks do NOT get better over time. However, one of the common exceptions is heavy clay soil. As the leak continues to hydrate more clay over a larger area, you may get enough swelling to reduce the leak further.
How deep is your pond at full pool? If you get an extended drought and your pond goes down 3', and the leak ceases at that point, then your fish are not really in much danger if your pond has sufficient depth.
I hope you enjoy your renovated pond ... despite the leak. It sounds like you paid good money to do it right the first time. It also sounds like your contractor got it 99% right, which is pretty good.
Fingers crossed for your second bentonite treatment.
If that works a little bit, then came back and post some more. There is another product called Soilfloc that may work a little better if you are getting partial success with the bentonite.
