Well water

• When treating your water, dealers don't always test for metals, which are especially present in well water and can cause your pool water and liner to turn brown or black.
  
  

Source water

• Some people do not test the source water before adding oxidizers such as chlorine, which can increase the pH or alkalinity of the entire pool. Remember, if the liner is stained, then the metal is no longer in the water and therefore will not show up in a reading.
  
  

Staining

• Even a small percentage of metals in your water will stain your pool liner.
  
  

Prevention

• To prevent your pool liner from staining, you can install a special metallic filter that removes the heavy metals from the water. This, however, will do nothing for the existing mineral content. If your stains are caused from metallic buildup in your water, using chemicals such as chlorine will not fix the problem.
  
  

Treatment

• Instead, adding vitamin C, or ascorbic acid, to your pool stains after the chlorine is discharged will serve as an antioxidant and will treat the stubborn stains. Do not go below a pH of 6.8--this can be problematic to your pool.