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I've been having trouble with this also this year. Last year, had a few spots of what I thought were MA, and cleared them up. This year, I'm using the pool much less (much cooler summer). It's mostly been covered up, and it seems that every time I want to use it, I have to do a major cleaning / vac job. Water has been clear all summer. There hasn't been any CC this year to speak of, so I thought that perhaps it's pollen (we're surrounded by trees, pines on my property as well as hardwoods in the forest across the street).
On this thread, I read that MA may not raise CC for the first time that I can remember.
Last weekend, the side walls had some green. So, I took the cover off and brushed and shocked. Started to let the FC go down but green on sidewalls again this morning so they got another good brushing. Right now, it's being shocked to MA shock levels again. I back washed the filter this morning and a lot of green came out! Usually grey comes out; never saw so much green before today!
Oddly, pool pH has gone from 7.5 (it's been about 7.5 - 7.6 all summer after I increased it from 7) to 8.