If the opportunity presents itself to empty the pond again and your not inclined to line the bottom, take some of the sediment out (good for garden - a good 3-6 inches), and then cover the fresh soil with a sprinkling of lime powder, this destroys the majority of bacterial forms, the good stuff will remain unaffected.
Once the pond has been refilled (a pump with small solar panel is superb for this) will put plenty of oxygen into the ponds bio-cycle and the fish won't be gasping like a raspberry dangler at beer drinking time in the late afternoon.
This should leave your pond in better shape and reasonably clear, adding a few lily pad type vegetation will allow the fish to hide and spawn. After a couple of days the water should be tested for its Ph level, this should be done before emptying and then directly after filling, and then a couple of weeks after that to give a comparison and shed a bit of light on what's happening under the water.
