A pool liner can be cleaned with either a bleach and water solution or by using baking soda. Maintaining the correct water chemistry is also essential to preventing stains.
Properly cleaning a pool liner requires knowing the cause of the stain. If the stains are green or brown, then they are most likely caused by organic substances, such as algae or other plant matter. Reddish brown colors most likely mean the stain is caused by rust.
Correcting the pool's water chemistry may remove organic stains without the need to remove the liner or do vigorous scrubbing. The pH level should be between 7.2 and 7.6, and the chlorine levels should be between 1.5 and 2.5. Calcium hardness levels should be at 200 to 300 parts per million, while alkalinity levels should be at 80 to 100 parts per million. When these levels are off-balance, the pool can be an ideal spot for algae or other organisms to grow. Cleaning the skimmer box and other problem areas with a rag covered in baking soda will not only remove some stains, but increase pH and alkaline levels in the pool.
Stains that cannot be removed through correcting chemical levels in the water should be removed with a bleach solution made from one part bleach and two parts water. Draining the pool and removing the liner is necessary for the solution to be effective. The solution should be applied to the liner and allowed to sit for an hour before rinsing. Additional scrubbing may be required. The process is repeated as needed to remove tough stains.