Airration would help with the oxygen level and help you use the depth of the pond. You mentioned the water quality with the near by trees. What is the ph level? My guess is low. As far as the geo system,talk with the installer. Are the lines just laying on the bottom or are the buried below?
Side note i just switched from geo to nat gas. My electric bills were crazy. Not the best system for cold climates. Its crazy how 70 degrees feels so much warmer now. Kinda hard to explain, you would think 70° would feel the same with either system.