What is the best way to deal with a pond lined with soil taken from dry ground, which emits methane bubbles nonstop when underwater? I'm concerned it's hurting life in the water.
Methane is produced from anaerobic bacteria. If you add enough oxygen to the water and make sure the pond doesn't stratify, aerobic bacteria should take over and produce CO2 instead.
Add a fountain to aerate the water to speed it up.