A pool liner is designed to mold into the pool's structure, protecting the pool's walls. High acid levels in the water can cause pipes or other metal fittings in the pool's circulation system to become corroded. Chlorine shock doses oxidize the corroded pipes and metal fittings, causing rust to form on the pool liner. It is necessary to promptly adjust the pH and total alkalinity levels in your pool water, and use certain solutions to remove the rust from the pool liner.
Drain the water out of the pool, since the water is contaminated with rust. Follow the pool dealer or installer's instructions to determine whether you should replace all of the water at once, or use progressive dilution.
Scrub the rust stains with a stiff pool brush. This will not completely remove the stains, but will help eliminate some rust on the pool liner.
Pour enzyme chemical pool cleaner directly onto the rust stains. Enzyme pool cleaners are liquid chemicals designed to dissolve dirt, oils, residues, and rust stains on pool liners. Refer to the manufacturer's directions on the bottle to determine how much cleaner to use. Allow the cleaner to absorb into the rust stains until foam appears. The foam signifies that the enzymes in the cleaner are reacting with the rust, turning the rust into a liquid form.
Wipe off the foam and remaining rust residue from the pool liner with a clean rag. Inspect the pool liner for remaining rust. Repeat the entire process if rust remains.