Once the metals are in the water, they don't go away, which is why you continue to have problems from it, and you are getting them from your well water, which you already know. The Pool Magnet that you're using only keeps it suspended in the water and off of your pool's sides. I believe that keeping your alk, pH, and chlorine on the lower side of normal ranges will help prevent the staining, but Marie is the expert--hopefully she'll be by soon to give you some more complete advice.
Janet
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