The most common cause of staining and discoloration of your liner below the water line is secretions by micro-organisms. As these micro-organisms feed, they secrete dyes, which can be one of many colors that stain the vinyl. Although these stains are unsightly, they in no way degrade the performance of the vinyl. These dyes are compatible with the plasticizers in the vinyl, causing the stains to go all the way through the sheet. There is no proven method for removing these stains.
There is a common misconception that the microbial resistant additives used in pool liners will kill the micro-organisms in the area adjacent to the liner. Many people believe that there is a "protective zone" near the liner that will not support life. This is not the case. The additive in the vinyl prevents the vinyl from supporting life but in no way does it prevent life in areas adjacent to the liner. Extreme care must be taken during installation to insure that there is nothing behind the liner that may become a food source for these organisms.
There have been cases of stains forming in pools soon after the installation of a replacement liner when there was never a problem with the original liner. Although there is no way that we can say for sure what has happened behind that new liner, it is believed that when the environment behind the liner is exposed to light and oxygen a "rebirth" or micro-organisms takes place. If the bottom and sidewalls of the pool are not properly treated, there is a chance that problems may arise.
There can also be changes in the ground water that introduce organisms into an area that had not been previously exposed. Extended periods of heavy rains will often cause significant changes in the microbiology of the ground water. Whenever there is a change in the environment around your pool, there is an opportunity for micro-organisms which hitherto were not present to move into the ground water, thereby creating the possibility of staining.