Sounds like when you cleaned the pond and removed the roots (I don't know what you mean by roots: from plants in the pond?) they were helping by leaching nutrients in the pond that grow algae (green plants that color your water green). Green water is not harmful, but your water sounds toxic to fish. They don't care what color the water is as long as they can breathe and the ammonia levels or chlorine levels aren't too high. If you live in town, you must put dechlor in the water when adding or filling. Since you did a total clean, even without scrubbing by adding water, the pond should cycle for a couple of weeks before adding fish again. If you have some cover like lilies, lettuce or hyacinth, they block the light that algae needs to grow. I had an almost 2/3 fish kill because I didn't vacuum the poo and solids out enough one summer in really hot weather. A bubbler along with filtration would be beneficial to your fish too, it just adds more air to the water.