I heard of this happening as a result of a heavy rain before, which can cause a few things to happen: Big PH swings, big PH swings as a result of the loss of buffer calcium in the water (extremely soft). You may wish to add limestone (dolomite) to the pond to help prevent this in the future. The other thing that can happen is a quick turn-over of the water column bringing nasty anaerobic water up into the places where the fish live. Unlikely in a new pond though.

Sorry this happened!