Depends on the actual biomass present but anoxic water forms faster with many fish, plants, other organisms, etc..
In a fish-heavy pond (Carrying capacity is reached) it can happen fairly fast.
Need to know what time of day aerator is being run?
It sounds like you had a hypolimnetic situation in place and possibly the aeration system wasn't strong enough flow to mix it, but the heavy rain most certainly was..
Rain is "usually" slightly slightly acidic (below 7.4). Run-off, depending on what it flows over before entering the pond, can cause yet other issues.
Perch (yellow) tend to handle slightly less O2 than some species but there are other factors.
Pumkinseed I don't know much about yet so I'll reserve that for others in the know..
Not knowing how you started up your aeration and it's capabilities, I "think" your rain event could possibly be the culprit.
