Just a thought. Sometimes deep water springs are supersaturated with nitrogen. Basically, you have to find a way to let the excess nitrogen escape. I suggest you try turning your waterfall back on and set up some sort of surface to "splash" the water before it hits the pond. Maybe some concrete blocks or other similar surface. It would be best if you could do this with the well water before it entered the pond. Not sure if this will help, but it might be worth trying.
