How Do I Clean Stubborn Algae Stains on Pool Walls?

Scrub with a stiff brush and use a chlorine-based stain remover to eliminate algae stains effectively.

Why Algae Stains Are So Stubborn

Algae stains happen when algae cells penetrate porous surfaces and leave behind pigments even after being killed. Brushing or shocking removes living algae, but not always the stains that follow. These stains may look green, yellow, or even black depending on the algae type and how long it has been there.

Algae can bond to rough surfaces like plaster and concrete, making them especially hard to remove. In some cases, the longer stains are left untreated, the more they calcify or embed into the surface, becoming part of the wall instead of just a surface stain.

Identify the Type of Algae Stain

Before cleaning, you need to know what you’re dealing with:

• Green algae: Often slimy and spreads quickly; easiest to remove.

• Yellow (mustard) algae: Clings to shady spots and is more resistant to chlorine.

• Black algae: Appears as dark spots; has deep roots and penetrates plaster.

Each requires a slightly different cleaning approach, especially when stains linger after treatment. Accurate identification helps avoid wasted effort and the wrong chemicals.

Tools and Materials You’ll Need

To fully remove stubborn algae stains, gather these supplies:

• Pool brush (nylon for vinyl, stainless steel for plaster)

• Algae-specific pool shock or chlorine granules

• Stain remover (organic or metal-specific depending on stain type)

• Algaecide (non-copper recommended to avoid future staining)

• Test kit for pH, chlorine, and alkalinity

• Pumice stone (for plaster pools only)

• Soft cloth or sponge (for vinyl)

• Protective gloves and goggles

• Bucket and stir stick (for pre-dissolving chemicals)

Step-by-Step: How to Clean Algae Stains

1. Test and Adjust Water Chemistry

Start by ensuring your water is balanced:

• pH: 7.2 to 7.4 (slightly low helps chlorine work better)

• Chlorine: 1 to 3 ppm minimum

• Alkalinity: 80 to 120 ppm

Balanced water helps your treatment be more effective and prevents scale or cloudiness during cleaning. Test strips are fast, but liquid drop kits give more precise results.

2. Shock the Pool

Use a high dose of chlorine shock to kill any remaining algae.

• Apply in the evening for best results

• Broadcast shock around the perimeter

• Run the pump for at least 24 hours

• Brush walls immediately after shocking

Use non-stabilized chlorine to avoid raising CYA levels. Repeat if chlorine is consumed quickly or algae persists.

3. Brush and Scrub the Walls

This is the most important step. Physically remove as much staining as possible.

• Use short, firm strokes on stained areas

• Brush twice daily for several days if needed

• Pay attention to steps, ladders, light niches, and shaded areas

For vinyl pools:

• Use only nylon brushes or soft cloths

• Avoid abrasive scrubbing that can tear the liner

For plaster or gunite pools:

• Stainless steel brushes are more effective

• Pumice stones can help rub out deeper stains

4. Apply a Stain Remover

If brushing doesn’t fully remove the stain, try a chemical stain treatment.

• Organic stains: Use ascorbic acid or enzyme-based removers

• Mineral stains (from copper or iron): Use a metal sequestrant

• Apply directly on the stain if possible using a sock or sponge

Let the product sit according to the manufacturer’s instructions. Continue circulating the water to help lift residue.

5. Vacuum and Filter Thoroughly

Once stains are treated:

• Manually vacuum loose particles

• Brush the surface again if needed

• Clean or backwash the filter

• Run the pump 24 to 48 hours

Debris left in the pool can allow algae to return. Use clarifiers if the water remains cloudy.

6. Follow Up With Algaecide

To prevent regrowth:

• Add a broad-spectrum algaecide weekly during warm weather

• Choose non-copper formulas to avoid additional staining

• Keep chlorine levels between 1 and 3 ppm consistently

Some products combine enzymes and algaecide for longer-lasting protection.

Deep-Cleaning Strategies for Black Algae

Black algae has protective layers that shield it from chlorine. To treat it:

1. Scrub the surface aggressively to break the outer layer

2. Use granular chlorine directly on the spot for targeted treatment

3. Apply a black algae cleaner if standard chlorine doesn’t work

4. Maintain elevated chlorine (3 to 5 ppm) for several days

Consider draining the pool for acid washing if black algae is widespread and persistent, but only as a last resort.

How to Prevent Future Algae Stains

• Test and balance water 2 to 3 times per week

• Keep chlorine steady and shock after storms or heavy use

• Brush the walls weekly, even if no algae is visible

• Skim debris daily and clean filters regularly

• Use a pool cover when not in use for long periods

You can also install UV or ozone systems that help sanitize water and reduce chlorine demand.

Maintenance Habits That Make a Difference

• Rinse swimsuits and equipment to avoid introducing spores

• Limit use of organic sunscreens or lotions that add biofilm

• Trim trees and bushes that shade parts of the pool

• Schedule weekly visual inspections and cleanings

Keeping your pool well-circulated and well-filtered is just as important as chemical balance.

Restoring a Clean, Healthy Pool

Algae stains might seem stuck for good, but with the right process and a bit of persistence, you can restore your pool walls to a clean, stain-free state. By pairing chemical treatment with physical brushing and ongoing maintenance, your pool will stay clear and inviting all season. Investing a few extra minutes each week in prevention goes further than having to scrub out deep, set-in stains later on.