I decided to empty my pool since my Ca hardness levels were so high and the pool water hadn't been changed in 6 years. Once the pool was empty the brown stains lightened up and looked more like rust stains. I decided I would try hydro jetting them off first with high pressure water and if that didn't work then I was going to try bleach and finally muriatic acid. The good news is that I was able to remove the stains quite easily in 30 minutes with the high pressure water. So I was able to avoid the chemical route. I'm refilling the pool right now.
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