The buffalo water treatment plant doesnt have an outfall into the canal.

If any treatment facility is the cause if increased levels, it is the county managed overflow relief facilities, which when they reach capacity, they will dump into waterways before treating collected runoff water, simply because they cannot.
The culprit to scajaquada & the canal is the facility located off of route 5 in hamburg/lackawanna, it is up stream from these water bodies. I have worked with the department of sewer & water management. This has always been the cause as only heavy rains carry various chemicals and run off to orfs. There are many articles also covering this.