I would doubt the water, only the first several inches will be warm. The lower water being much more dense will remain cool, and the fish will stay where the prefer to be. That is unless you have so much water flow and wind that the water is mixing, and with that kind of difference, it would require your pond looking more like a river.
It is probably the dark water coming in, which is sort of worrisome as in sewage? Over-stuffed septic tank?
