I fill from city water and do not have any stains in toilets. My tap water has a high ph and cya if that helps. Since I had no reply I had to go back to pool store. I used more stain remover and the some special floc that starts with an R. It has helped. my liner is not brown but water is very cloudy. A whole lot of junk fell to the bottom and I vacuumed it to waste.