Yep. Pond leaks are a pain in the posterior.
Step one is to correctly identify the problem. That is often very difficult to achieve.
The correct subsequent steps depend on getting Step 1. right.
Sometimes it is not even possible to identify the problem and you just have to treat the "symptoms".
If you can't exactly pinpoint your leak, another option is to "scarify" (disc or till) the bottom as deeply as possible to break up the existing flow paths. Then wet the churned subsoil and compact as heavily as possible with a towed sheepsfoot roller or with a self-propelled vibratory soil compactor. (The rental for a Caterpillar CP563 is only $1,000/day in my area, but it will cost you more than that with trucking.)
You might be able to compact the bottom of a 3-acre pond in two days(?) if you had a helper that was wetting areas in front of you. That MIGHT seal your leak. If it didn't, then I think any partially sealing that resulted would only help a soilfloc treatment work better. (I would definitely talk to TJ before investing any more time/money.)
There are some dirt contractors on the forum that could give you more accurate information on the method I described above.
