I have 1 pond that had this problem during named tropical events (even with 4 staged drain over flow pipes). I corrected this by building a breeding / sediment pond upland to slow down the duration of the water from the watershed reaching the lower pond to allow the 4 over flow pipes to handle the load. Have not had water go out the emergency earthen spillway in the 20 years since.
BTW having picked up adult fish in the pasture during tropical events was clear indication that no matter what you will loose some fish. During hurricane Opal we just tied a net to the fence to catch enough for a fish fry.
