I am unfamiliar with your specifics as to climate, location, fish species or water quality. Autumn in my area often brings low water, somewhat high water temperatures and low dissolved oxygen that can stress some fish species. Lentic and Lotic conditions of a fish farming operation are likely to be affected differently. Storms can bring in excessive loads of leaves and other organics during freshets, non-point pollutants and biochemical oxygen demand increases. Some intolerant aquatic insects as sources of fish food may also be affected, which could be monitored as to species and abundance. Some aquatic insects and fish species are more tolerant than others of pollution, stress, low water quality. If food is lacking, some predation may be occurring, or possibly water birds, animals as raccoons, otters, etc. may be actively feeding getting ready for winter. If your University or other local agency has a limnologist or fisheries biologist, they are likely to be especially helpful and knowledgeable as to your specific conditions and species. Autumn may also be a period where blue-green algae could become a problem. Water quality tests might bring up other issues relative to pH, alkalinity, or certain chemical toxicity, etc., pertinent to the autumn conditions. And sometimes fish under temperature or oxygen stress actively seek out the best conditions, such as where cool tributary, spring or groundwater enters, or deep pools below aerated riffle sections.

How old is the fish farm and how recent is the phenomena?

If it is a new phenomena, what has changed recently (e.g. did you change the fish food recently? Have the oxygen/temperature levels in the water changed recently?)

If you are using fresh water and the oxygen levels have fallen recently, you can use a plastic pipe to a higher water source (e.g., a mountain stream) and a venturi fitting to draw in air to the water to highly oxygenate the water). The higher water source can also cool the water in the fish tanks/ponds. Adding shades over the tanks/ponds can also cool the water in the fish tanks/ponds.

If it is a long-term phenomena, you may be fighting millions of years of evolution and you may be able to reverse it via selective breeding for fecundity and growth during the autumn.

env variables like temp. has an effect