I can see your point! I have a well, and never have to worry about running out of water, so it didn't enter my mind. The stains on your liner are probably from organics and will fade out with the high chlorine levels - they won't come off with regular scrubbing - the way you can tell if they are organic is if they rub off with some chlorine. If they are metal they will come off with Vitamin C (ascorbic acid) or ph down. You can crush them in a sock and rub them on the stain. My guess is they are organic from the stuff lying on the liner and it will take a couple of days for them to fade. As they say "patience in a virtue" Best of luck, let me know if the stains don't fade.