Should your pool develop spots and discoloring chances are the most common cause is algae. Checking the your chemical levels, adding an algaecide, and brushing the pool should prevent this problem. However, if the stains are persistent, you should check the p-h and alkalinity levels, as they are probably too low. These stains are the results of minerals that have condensed out of the pool water. Scale formation is another cause of discoloration. It appears as a rough spot. Scale on the pool is the result of p-h and alkalinity levels which are too high. Once you make the appropriate chemical adjustments to cure the problem, scrub the stains and treat with a cleaner that's safe for your pool. If necessary, you may need to drain the pool and refill it with fresh water. The color of the stain can help you determine the appropriate cleaner, as different colored stains are created from different minerals. Your local pool consultant can provide additional information on removing stains and spots.
