Good question I run into that situation up here quite often. We do not have limestone but sedimentry blue stone it depends on how the vain of the rock is running and how much there is in the shallows we leave it alone. In deeper parts of the pond it is a call that depends on water feed and springs when we dig the deep holes in the pond are dug first and then we will let them sit and see how much water loss we get due to rock formations if it is alot will cap with a 2 foot bed of clay and moveto another spot and try for better results.
It is hard for me to explain on this board unless my feet are planted on the soil you are moving and the surronding terrain. I have dug ponds with rock bottoms and they do just fine with their existing water supply,and others have a hard time maintaining constant water level.
I would say 70% of the ponds we build are on the side of a mountain and it takes alot of thought and planning . My dozer man is amazing he shares the same vision of the finished pond that I do 90% of the time, the other 10% is begging him to get a little deeper.
When building a pond with rock bottom the key factor is water supply year round and if your soil can retain the water

Good luck


Scott Trava
Catskill Pond
http://catskillpond.com
scott@catskillpond.com
Returning Catskill Waters To A Simpler Time
EST. 1923