Had a mustard algae problem....looks like it's in the cover

I've had an on and off mustard algae problem for a month. I didn't shock for a long enough period I think, but another problem I noticed is some of the bubbles in my cover are popped, and they are filled with yellow water. It's just a few here and there, looks like the holes got there from scraping the side of the pool when taking the cover off. Do I have to get rid of the cover?
 
You may not need to dispose of the cover, but you certainly do want to ensure any old, stagnant water that may be trapped in any bubbles or pockets are removed and cleaned. If you can scrub, power-wash, and/or bleach/disinfect that cover that might help. I certainly wouldn't throw it back over the pool if there's any chance it may release algae-trapped droplets back into an otherwise clean pool.

As for any potential algae in the pool, now is the time to SLAM. Use your TF-100 or Taylor K-2006 test kit to do it thoroughly and accurately, following the SLAM page (link below) in its entirety to rid your pool water of any algae.

Hope this helps.
 
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