We had the same problem with some acreage my family purchased about 10 years ago. The pond would fill up after a heavy rain then it would just leak out. The pond was a similar size as what you describe and also was heavy with a clay base. We found out about a product that is produced or mined in or around the Malvern area to solve the problem. Unfortunately thats been 10 years ago and I forgot what the stuff is called but it works. Its messy as all get out but the pond was never low again, other than in the heat of the summer. The stuff came in bags like concrete and it had the texture and look of lime. When its thrown or spread over the water by the dam it became a real sticky clay like substance that wass sucked into the leaks stopping them forever. I will ask my dad if he remebers the name of the stuff. Hopefully I will catch his dementia on a good day and he will remember. If not I hope I at least gave you something to investigate to help you solve the problem.