Most populations will handle it just fine.
As it comes down, there will be some incidents of fish getting isolated in side eddies which become separated from the stream, and they may die. But the number that wind up in this situation will be a small % overall. Go fish the side eddies and see if you can rescue a few. I've done it before, even resorted to bait (it was for the good of the fish!!!!!)
There will also be individual streams which experience acid spikes, however, I think that usually kills eggs, not fish, so in this case the timing isn't bad at all. The worst floods for this are usually early spring, when you get heavy rain on top of snow and frozen ground, the water is almost solely surface runoff unfiltered by soil, and the eggs are still unhatched.
There will also be changes in the structure of streams, some holes fill in, new ones are formed. Some spots get flushed of sediment, others get a dumping of sediment. Bugs especially are dependent on bottom type, so they will be effected more than fish. Some hatches may be weaker, some stronger, and in different places. So that hole that was an excellent sulfur hole this year may not be next year, but the other hole that wasn't a good sulfur hole may improve in a year or two.
In the long run, this kind of change is generally good, streams need a good scouring now and again. And I remember with the flooding associated with hurricane Ivan, a week or two later after the runoff subsided, we were left with supercharged aquifers and groundwater, which made EXCELLENT fishing in limestoner and freestoner alike. The water was ridiculously high, "blown out" by any other measure, except it was also clear.