When organic matter settles to the bottom or sides of a pool and is allowed to sit for awhile, it tends to stain the surface. Acorns leave small brown spots on the bottom of a pool, but never the sides, as acorns won't attach to the walls like waterlogged leaves can. The stains are caused by the tannin content in the acorns.
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General Organic Stain Removal
Many organic stains will fade on their own after several weeks once the staining agent has been removed from the pool. All acorns must be removed from the pool before beginning any cleaning process. If you do not remove the acorns, they will resettle in another place on the pool's floor and will create a new stain.
Chlorine works very well to remove stains from the tannin in acorns. If you only have a few stains in your pools, the easiest and most effective way to clean is to use a chlorine tablet. Take a long pole and attach a chlorine tablet to the end of it either with wire or waterproof tape. Scrub the stain with the tablet and it will be removed.
Large Area Cleaning
When you have numerous stains on the bottom of your pool from acorns, using a rod with a chlorine tablet on the end of it will be too time and labor intensive to be truly effective. Instead, apply powdered chlorine to the bottom of the pool and allow it to break down the stains on its own. This method will take longer to remove the stains.