Kris,

If the pond held water well before it was dug out and the dam raised, then those actions are most likely the cause of your leak(s).

I suspect they either dug through the original clay seal or damaged the area around the overflow pipe. (Is there a bottom drain?)

When the pond re-filled and then drained did you notice a wet area around the overflow pipe exit or at some low spots on the downstream side of the dam? If not, then I will discuss piercing the original clay seal - but that doesn't mean that is the cause of your leaks.

A silty clay loam with 21-27% clay should be a suitable material to form a good seal. However, even good material must be scarified and then compacted.

Basically, your original soil profile was composed of many separate layers. Some may have been 50% clay and some may have been 97% sand with only 3% clay. That thin sandy layer is capable of leaking a lot of water. (Your average is 21-27% clay!)

When they originally built the pond, they probably disked or tilled the bottom of the pond to a depth of 12-18". This breaks up and disrupts all of the layers, which were then compacted to form the seal.

When they dug out the pond again at the later date, they may have excavated through this seal in a few spots. However, that is all it takes to cause a leak if you have any layers with high permeability.

Do you have heavy equipment on your farm? If so, then one possibility is for you to continue drying out the pond. You can then disk the bottom and sides (where safe) with your own equipment. You might be able to compact with whichever vehicle has your highest ground pressure at the tires. However, it would be much better if you could pull a sheepsfoot to compact, or rent a vibratory soil compactor (like a self-propelled padfoot roller at $500-$800/day). You will need a way to spray water on the soil during your compaction work.

Keep working with TJ and follow his suggestions. However, if you could solve 90% of the leak problem with disking and re-compacting, then a proper sealant application would be much more likely to get you close to 100%.

Good luck on your project!