No, you aren't missing anything. Thermoclines set up at different depths in different bodies of water, and in different depths of the same body of water. They don't set up until the upper water column gets much warmer than the lower water column, which is mainly a Summer deal. When Fall temps start dropping, the upper water column gets colder (cold water is heavier than warm water) and drops down into the lower water column, mixing the temps & oxygen content. This is called "turnover". The thermocline won't appear again until the following Summer warm up, so it's not a concern during the late Fall/post turnover time thru the late Spring/early Summer warm up time.
And, yes .... you are correct that fish will not stay "below" the thermocline depth, as there is not enough dissolved oxygen at that depth to sustain much activity.


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