I am NOT a pond building expert, but I am a geologist.
You have observed gravel layers in close proximity to clay layers. That means your soils are unpredictable. IMO you are going to have to dig at least 12" past your bottom and side slopes in all locations and then backfill to the final grade.
USDS Pond Handbook #590 states:
"Generally, soils with at least 20 percent passing the No. 200 sieve, a Plasticity Index of more than 10 percent, and an undisturbed thickness of at least 3 feet do not have excessive seepage when the water depth is less than 10 feet."
("Passing the No. 200 sieve" means 20% clay content.)
Basically, if you leave your bottom in undisturbed clay but it is only 6" thick above the next gravel layer, then your pond will probably leak.
The other consideration is that soils in place are already compacted!
Some of your clay areas almost certainly have thin layers of sand or even gravel situated within the bulk clay. These layers will allow water to leak out of your pond.
Generally, you cannot use compaction to get rid of these permeable layers. The soil must be "disrupted" and then well mixed prior to compaction.
"Scarify the soil to a depth of 16 to 18 inches with a disk, rototiller, pulverizer, or similar equipment. Remove all rocks and tree roots. Roll the loosened soil under optimum moisture conditions in a dense, tight layer with four to six passes of a sheepsfoot roller in the same manner as for compacting earth embankments."
Can you spoil the gravel outside of the pond?
If so, then I would stockpile clay in the bottom of the pond while working to get the gravel out. Cover everything in a 6" lift of material with decent clay content and compact. Then do the same thing again with another 6" lift of material.
You DO NOT need pure clay for these sealing blankets! However, 20% clay content is the minimum. You should be able to moisten the blanket material and roll a thin "worm" between your palms.
Hope that helps. Good luck on your new pond project!
