If you apply enough lime you should raise the PH enough to make it lethal to the fish.

I will probably get scolded for this but another option is Clorox Bleach after the liming (the liming is good for the pond bottom so don't forego it). You could direct a hose to each water hole, and with a funnel on your end dump bleach into each hole -- if you can't reach the holes by foot.

Although very toxic to fish initially the Clorox disapates very rapidly. I did this in a very small holding pond to kill the snails that had migrated to the remaining water left. They seemed to be impervious to a lime treatment.

Another option if it gets cold enough in you area in winter is to just let the pockets freeze after you have draw down as much water as possible.

If pigs could fly bacon would be harder to come by and there would be a lot of damaged trees.