How to Remove and Prevent Pool Stains (Iron, Algae and Other Stains)

Do you ensure that the pool water is balanced, and you still have stains in your pool? Why is that, and what is the best way to remove the stains without damaging your pool?

Pool stains are deposits from algae, rust, or lime (calcium). These arise either from a lack of disinfectant or from a chemical overdose. With a pool brush, a bit of chlorine, and the proper water treatment, all stains in the pool will disappear.

In this article, I explain how stains are formed in your pool and which pool equipment can remove them.

What causes pool stains?

There are several reasons why pool stains appear.

The most common reason for swimming pool stains is a lack of disinfectant or a short filter run time.

A difference is made between two types of pool stains:

  • Organic stains: Leaves, grass, insects, fruits, etc., provide bacteria and algae with a source of nutrition and lead to stains in the pool when organic substances remain in the pool for a longer period.
  • Inorganic stains: Well water with a high iron content or an incorrect pH level lead to rust or limescale deposits in the pool.

The distinction is not trivial, as a suitable cleaning method and agent against pool stains should only be selected after being determined.

In the following chapters, you will find out how to identify the spots in your pool and what causes are responsible for the appearance of stains on the bottom and on the pool walls.

Green spots in the swimming pool

  • Green algae infestation (organic)
  • Slightly green to dark green in color

If you discover green spots in your pool, there is a high chance of green algae.

You can recognize this type of algae by local growth in the corners and walls.

The algae are initially light green and turn dark green over time.

Green algae grow quickly and turn your pool green overnight if the water treatment is poor and the filter run times are too short.

Storms with rain and humid air promote algae growth in your pool – despite optimal water levels.

Fortunately, the green algae can be removed quickly – you can find the instructions below.

Black spots in the pool

  • Black algae infestation (organic)
  • Dark spots on the floor and on the walls

If the black spots are isolated dots or large-scale deposits, this could be black algae (also known as blue algae).

You can check this by pouring some chlorine granules onto a small area in your pool. If the black color turns brown, then it is organic stains.

Another indication of black algae is that it is difficult to remove with a brush.

And how do these algae get into your pool?

Black algae are usually introduced into the pool through dirty bathing suits.

However, the black pool stains may be caused by a high proportion of manganese and iron in the water and appear as black spots.

Tip: If you discover black to dark blue stains on the pool liner, it is not necessarily the blue algae because this predominantly grows in concrete pools.

Reddish-brown spots

  • Probably organic debris
  • Reddish spots on the pool floor

Take a pool brush and see if the red stains come off easily.

If so, then it is very likely that these stains are organic.

You may have blueberries growing nearby and causing stains in your swimming pool.

Tip: If there is too much algaecide, reddish-brown stains can form in your pool and cloud the water. In my blog post, I explain in detail how the algaecide works.

Yellow spots in the swimming pool

  • Mustard algae in the pool (organic)
  • Local growth of algae or yellow border in the pool

Yellow algae in your pool are relatively rare, also known as mustard algae or golden algae.

You can recognize this type of algae by the yellowish mustard color. However, in the early stage, it can be confused with the green algae.

Most corners are infested first, and a yellow border forms in your pool.

The yellow algae probably get into your pool via a host – ducks and other animals – or by pollen.

Ineffective disinfection of your pool water and short circulation times encourage mustard algae to grow in your swimming pool.

Pink spots in the pool

  • Bacteria in the pool (organic)
  • Pink stains in the pool and on the filter

Most pool owners speak about pink algae when they see pink or red spots in the pool. However, these are not algae but bacteria.

The bacteria cannot be visually recognized immediately because they are initially transparent. Typical pink-red stains appear in the pool only after using disinfectants like chlorine.

These bacteria (pink algae) often make themselves noticeable through slippery surfaces.

How the bacteria – or pink algae – arise is not clear.

But you should know that these pink spots in your pool are harmful to your health.

Brown spots in the pool

  • Manganese or iron deposits
  • Extensive infestation in the pool

Brown spots and cloudiness are caused by a high proportion of manganese or iron in your pool.

Mostly this is the case after filling the pool with well water.

However, it is also possible that rust falls into your pool from a nearby fence or other objects.

If there are no leaves in your pool, which causes the brown coating on the pool bottom, you can assume that the water has a high iron level.

White spots on the floor

  • Deposits from flakes or bleach stains
  • Easy to remove dirt on the floor

White spots on the pool floor are caused by flocculants that have not been filtered or incorrect use of chlorine tablets.

You can recognize the flakes because they can be easily swirled up.

In the case of white spots on the pool liner, chlorine spots (bleaching spots) can be assumed. If the stains are bleaching spots, you have to live with them.

The bleaching stains often occur in vinyl or PVC pools that are chlorinated using a floater (metering float).

How to get rid of pool stains

Identifying the spots in your pool and clearing up the cause is only half the job.

I will show you how to remove the pool stains in the next step.

If you want a quick overview, the table shown here will help.

Pool stains Solution
Organic stains on the floor
  • If possible, scrub off and let the filter run.
  • Sprinkle locally with chlorine granulate and let it work for 24 hours.
Organic stains on the wall
  • Scrub with a pool brush.
  • Perform a pool shock and let the filter run for 24 hours.
Inorganic stains in the pool
  • Test the water on metal.
  • Use a metal pool stain remover.
  • Use hydrochloric acid and optimize the pH level.

Detailed instructions on how to remove inorganic and organic pool stains can be found in the next chapter.

Remove organic pool stains

The most common stains in the pool are organic and can be removed with simple means.

A pool brush and the filter pump will often do the job, but you have to take stricter measures in other cases.

How to remove organic pool stains from the bottom:

  1. Test and optimize the pool water: Use test strips to measure the current water levels ​​in the pool and optimize them if necessary. The pH level should be between 7.2 and 7.6, the alkalinity between 80 and 120 ppm, and the calcium hardness between 200 and 400 ppm.
  2. Do a local pool shock: For small stains, sprinkle chlorine granulate locally on the floor, and for large stains, the pool should be completely sprinkled. Let the chlorine sit for 24 hours with the pump turned off.
  3. Scrubbing the pool: After 24 hours, the pool must be cleaned with a pool brush.
  4. Start the filter system: Let the pump run for 24 to 36 hours until the water becomes clear again and the chlorine level sinks below 1.5 ppm.
  5. Check your pool: Are the stains gone? Perfect! Otherwise, repeat the process again.

Tip: You do not necessarily have to do a pool shock in the case of pool stains from leaves or light residues from green algae. But if you have to apply a shock cleaner, read through my instructions about the pool shock beforehand.

Scrub the stains and let your pool filter run for a few hours.

To remove organic deposits from pool walls:

If there are stains on your pool wall, it is impossible to apply chlorine granules locally.

In this case, you have to clean your pool differently.

  1. Testing pool water: First, you have to test and adjust the water levels in the pool ​​- see above.
  2. Use the pool brush: Before the shock chlorination starts, the deposits must be removed from the wall with a pool brush so that the chlorine works better.
  3. Shock the pool: Now, use liquid chlorine and pour it into the nozzles of the return flow of the pump. Depending on the concentration, 5 – 10 liters of liquid chlorine per 25 m³ of water are sufficient.
  4. Use flocculant: It is advisable to use a flocculant in addition to chlorine.
  5. Let the pump run: Start the pump and run it for 24 – 36 hours – if necessary longer until the water clears again.

Tip: I recommend doing the pool shock late afternoon or in the evening. It is important to have the correct concentration of liquid chlorine to avoid an overdose in your pool.

Remove limescale and iron deposits in the pool

Stains caused by limescale or iron in your pool are more challenging to remove but not impossible.

Remove inorganic deposits such as lime:

  1. Switch off the pump: First, switch off the pool pump.
  2. Put on protective equipment: It is essential to wear protective goggles and a protective mask for your own protection.
  3. Remove slight limescale: Apply the hydrochloric acid (pH minus) to a sponge and wipe off the limescale from your pool liner.
  4. Remove limescale in the filled pool: Pour the acid in the appropriate places in the pool and let the water rest for 1 day.
  5. Scrubbing lime: After the acid has taken effect, first scrub the walls and then the floor.
  6. Vacuum the pool: Finally, you have to vacuum the pool with a pool vacuum.
  7. Optimize pH: Use pH-Plus to adjust the pH level. This should not exceed the limit of 7.6 – otherwise, lime will form again.

Tip: You need 5 to 10 liters of hydrochloric acid per 25 m³ of water against the lime. You should also measure and adjust the pH level after every rain.

Remove iron deposits and rust in the pool:

  1. Test the water: Test the pool water for the iron level using a suitable measuring method.
  2. Buy a metal stain remover: If you know what kind of metallic stains occur in the pool, then you can buy a special pool stain remover.
  3. Follow the instructions: Since every stain remover works differently, read the manufacturer’s instructions and follow the instructions.

Tip: Rust stains and other iron deposits should possibly be cleaned in the pool after the winter, even before the pool is filled.

Prevent pool stains

After the organic and iron deposits have been removed from your pool, preventive measures should be taken to prevent re-staining.

Organic deposits in your pool water can be prevented with little effort.

All you need is a pool maintenance routine:

  1. Pay attention to the water balance – the pH level, total alkalinity, and calcium hardness – are correct.
  2. Let the filter system run through daily for 6 – 8 hours and, if necessary, optimize the nozzles to prevent dead zones in the swimming pool. Add a flocculant when filtering.
  3. Regularly clean the pool with the pool brush. Alternatively, you can use a pool robot against deposits.
  4. Use a skimmer and a pool net to remove leaves, insects, etc., from the water surface so that they do not end up on the ground.
  5. Remove plants that bear fruit and fall into the pool.
  6. Regularly check for stains in the pool, and don’t wait long to clean the pool.

Extra tip: rinse the filter monthly or clean the cartridge filter.

Prevent iron and rust stains in the pool

  1. Regularly test the amount of iron in the pool water and use a flocculant to prevent it.
  2. The pH level should not fall below 7.2 – otherwise, corrosion will quickly form in the pool. In addition, an optimal pH level favors the filtering off of iron.
  3. Ensure that the pH does not rise above 7.6 – otherwise, limescale will build up in the pool.
  4. Check all pipes in the pool for rust residues and other damage, such as scratches on steel wall pools. These parts may need to be repaired or replaced.
  5. Change the filter sand annually if it is used too heavily.

Info: Pool products against water clouding are not stain removers for rust. You can only bind the metal ions and prevent deposits.

Conclusion on how to clean pool stain

Every pool owner has to struggle with stains in the pool, but once the cause has been found out, the stains can – in most cases – easily be removed from the pool.

This works for most organic stains, but sometimes a sweaty pool maintenance is necessary.

Therefore you should always pay attention to an optimal water balance and try as best as possible to prevent stains in your pool.

After all, it is said: Prevention is more manageable than cure.

It is best to always have the right pool cleaner on hand for this purpose.

If you have any further questions about pool maintenance, I recommend my helpful search function.

Alternatively, you can write to me at @contactswimfool on Twitter. I will help you personally.

Good luck with stain cleaning!

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Hi. I'm Max Berg. I've been in the pool industry since 2015 and have always felt drawn to water. I'm the author behind, where I share my years of experience in pool maintenance and give helpful tips on keeping a swimming pool or hot tub clean. My tips reduce the costs of water treatment and protect the environment.

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