While all stains are either mineral or organic, 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 [...]

This is a tough question. Below is a suggestion from one of the product engineers at the plant that makes the actual vinyl sheet.
The following approach could be used to narrow down the possibilities; however, there is risk of damage to the print pattern and liner material in doing so.
First, try direct contact on a [...]