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.
Some types of bacteria and fungus found in the soil can actually penetrate through a vinyl liner and cause stains to appear on the liner. Usually they will start off as spotted or cloud-like formations on the liner. Algaecides used in the pool water have little if any effect on the stains caused frombacteria, since it does not get to the source of the bacteria in the soil.
In most cases, these three problems are different stages of the same phenomenon. The cause of these problems are many and varied, but have a universal theme.
There can be many contributing factors that lead to the fading of your liner. All of those factors can be grouped under the heading of chemical attack, however the leading cause is simply over chlorinating. Just as excessive use of bleach will fade your clothes, over chlorinating of your pool water will greatly accelerate the fading of your liner.
What is the most vinyl friendly way to winterize a vinyl lined pool? It is fairly simple. Use the absolute minimum amount of chemicals that will allow the desired effect. Do not shock your pool using Trichlor (hypochlorite is safer) and circulate the pool water for 72 hours before shutting down.
Most people put off the process of opening their pools until it is time for it to be used. Therefore, when the pool is first uncovered, the pool water is usually an ugly shade of green. So what is the natural tendency? Throw a ton of chemicals in the water to clean it up as soon as possible. This is exactly the wrong way to go about it.