On digging your new pond and the soil you are working in. If you have that rock layer, and the way you describe your underground water source, when you dig the new pond next to the old one, it may turn out that as you are pumping that water out to dig, the water from old pond will be flowing into the new dig. Are you prepared to lower that pond level down to the clay level, where this won't be happening?
If the water flow don't happen that way, I would dig the new pond lower than the first. Break the barrier, then when the water was lowered in the first pond from doing that, clean-up edges and things you might want to do(habitat, docks, etc.)and possibly dig a second hole deeper (if possible at that point).
