The other thing that comes to mind is temp change in the water. Maybe all that rain was so much cooler it just cooled your pond down to fast specially in the shallow areas. I don't know just thinking out loud. That is another reason I like having my air running during heavy rain events to help keep a better all around temp of the body of water.
Fresh water fish are more adaptable to water temps changes but to what extent before they start having issues? It may very well been a combination of these things that did you in.
If you can afford it I would definatley get air in your deeper spot in your pond and maybe one more setup elsewhere in the pond.
RC
