This is what the pond folks call Summerkill.
Summerkill is an oxygen depletion event. Most fish prefer an oxygen concentration in the water above 4 parts per million (ppm), but sometimes, during the heat of late spring and early summer, a layer of oxygen poor water may form at the bottom of the pond. This bottom layer will be cooler, darker, and may smell bad. If the water on the bottom contains less than 2 ppm of dissolved oxygen the fish will try to stay out of it, even if they are a species that prefers cooler temperatures (i.e. goldfish, koi). Bacterial decomposition of organic material causes this "bad" water. This condition occurs more frequently in deeper ponds, where excess water flows off of the surface layer. The bottom layer slowly accumulates while any overflow comes from the top. 

Summerkill is often triggered by a hard rain, causing the top and bottom layers of the pond to mix. After mixing, the pond may change color from its normal green to brown. This mixing may happen a day or two following the rain, and the subsequent drop in dissolved oxygen need only occur for a short time to kill fish. It may happen at night. Chances are that the oxygen concentration will have already increased to normal levels by the time you discover the problem.

The best strategy for dealing with this situation is to prevent the buildup of the lower, oxygen poor layer, by keeping the pond water circulating. This can be done by adding a submerged pump, a decorative fountain or an actual filter. 

Additional Resources

http://plants.ifas.ufl.edu/guide/fiskil.html