There are stain removers they sell in pool stores. These usually are some form of citric acid or ascorbic acid. I would suggest you add enough sequestering agent as per bottle (this is a metal out, or metal free chemical). While you ph is not any higher than 7.2 and let it run for a while. Sometimes this will lift the stains. If they don't lighten enough after a couple of days then you can use the ascorbic or citric acid treatment. There is a sticky on the top of this forum that will explain how to do it. Feel free to ask any questions. I usually try the metal out first, cause you need to have it in your water when you do a stain treat anyway!