There are three main causes of what appears to be staining or marks on a pool interior surface.
The first, and most common cause of staining or discolouration of a pool interior is algae. This will start in an area where water circulation is not good, like the deep end or comers of the pool.
Or, it could be caused by algae feeding off debris in an area from overhanging foliage or just a basic lack of enough chlorine to maintain the water balance.
By the addition of an algaecide or a super dose of chlorine, the algae will die and then it can be brushed off the pool surface and permanently removed. Some more stubborn types of algae like black spot, need to brushed before the addition of chemicals as their outer surface forms a protective barrier to chemicals.
By brushing and breaking the outer surface, it allows the chemicals to more easily kill the algae so it can be removed. Provided the correct chemical levels and good water circulation are maintained, it will be removed permanently.
The second type of staining is from metals in the pool water. These metals can be introduced by ionic sterilising systems or even from a water source (town water through an old copper pipe or bore water) that contains a higher than normal level of metals when filling or topping up the pool.
If increasing the acidity (lowering PH in the pool) removes the staining temporarily, then it indicates a problem with metals. If you re-adjust the PH and the stain re-appears, then this confirms it is caused by a high concentration of a metal in the pool water. Lowering the PH just puts the metal into solution, it doesn’t remove it from the water and that is why it will re-appear when the PH is balanced – it precipitates from solution and plates onto the pool interior surface.
To remove the metals, you need to dilute concentration by using a chelating agent or draining a substantial amount of the pool water and re-filling with fresh water (without metals).
The third, (and very rare cause of staining), can be microbial activity under the interior surface of the pool. If in this example the pool has a PVC liner, it is possible for ground water contamination under the liner to encourage microbial activity. These microbes feed off nutrients in the ground water (like seepage from a septic system or other grey water) and they secrete dyes that will stain the liner from the underneath and can flow through to the inside surface of the pool.
Once this dye staining has occurred, the stain can be lightened sometimes with the addition of high levels of chlorine introduced into the pool, but usually the staining is permanent and cannot be removed.