How to Clean Pool Liner Stains: 5 Tips to Get the Job Done Right

To clean pool liner stains effectively, identify the cause, shock the pool for organic stains, use a metal stain remover for metal stains, scrub with a proper pool brush, and establish a future cleaning schedule for maintenance.

how to clean pool liner stains

Swimming is a luxury to many, and stressing about the state of your pool may ruin this relaxation. While you may be adamant about keeping your pool well-maintained and clean, your pool liner can still get stained from time to time. 

With that considered, you might be wondering how to clean pool liner stains. Here are five tips to remove pool liner stains swiftly and effectively! 

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1. Discover the Cause of the Stain 

There are a wide variety of reasons why pool liner stains appear. The two main categories of pool liner stains are metal and organic. Depending on the appearance and color, you can determine what caused the stain. 

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Stains triggered by metal are primarily related to the water source or corroded copper pipes. Additionally, rusted pool gear can be a culprit. 

Various metals will create different-looking stains on your pool liner, with colors between iron and manganese markedly different.

Stains that are red or brown are associated with the presence of iron in the water source. In contrast, purple and black indicate manganese is the culprit.  

The natural environment surrounding the pool can stain a pool liner as well. Berries, pollen, leaves, and other natural debris fall into the organic category. 

As stated above, determining the color of pool liner stains can help you figure out the source of your pool stains.

Typically, if a plant or natural debris gets into a pool, you’ll likely encounter pool line stains that are green or brown-colored in appearance. Pool liner stains made by berries found in nature are red and blue. 

2. Shock Your Pool To Treat Organic Pool Liner Stains

Pool shock treatments have strong chemicals, such as chlorine, that rid the pool water of harmful pathogens.

While it is wise to shock a pool weekly when actively used, this practice can also be beneficial when removing organic pool liner stains. 

Organic stains that seem new and small will likely disappear after one round of pool shock. That won’t be the case if the pool liner stains are large and older. Instead, shocking the pool with a more concentrated shock treatment will be the most effective. 

It is important to note that you should wait at least 24 hours after the shock treatment to take another dip in the pool. This waiting period is crucial due to the harsh chemicals, to which you don’t want to get exposed. 

These chemicals can impact your health, ranging from skin or eye irritation to lung problems. If you drink the water, you could become nauseous and start vomiting. Thankfully, exposure to pool cleaning chemicals shouldn’t have long-lasting effects.

3. Use a Metal Stain Remover for Metal Pool Liner Stains 

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Unlike organic pool liner stains treated with pool shock solutions, metal pool liner stains can be more challenging. Thankfully, numerous products have formulas that exclusively treat specific metal pool liner stains. 

These potent stain-removal products are designed to target even the hardest-to-remove stains and restore pools to their pre-stain appearance.

To get the most out of these kinds of products, you’ll want an at-home test that can help you figure out which metal is causing your pool liner stain. 

While determining the cause of the pool liner stain with color is a straightforward and quick option, an at-home test will be much more precise. 

At-home stain tests are easy to find at many pool supply shops and can be bought online.

If you own the pool and don’t feel comfortable or confident performing this at-home test, your local pool supply shop most likely offers this service. 

4. Scrub the Pool With Proper Pool Brush 

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When considering how to clean pool liner stains, one option to properly remove a pool liner stain is to apply some elbow grease to the stained area!

This step should happen after shocking the pool or treating it with a metal stain remover solution. 

After adding the cleaning solution to the water, leave the liner stain alone for several hours. Once it’s time, start scrubbing the pool liner stain with a pool brush harshly to remove the excessive color that may have been left behind after the initial treatments. 

The type of bristles a pool brush has is critical to how well it performs. The pool brush bristles should be tough and resilient enough for frequent use. 

You might opt for a nylon or poly bristle brush for new stains. Nylon and poly bristles are known to be gentle on your pool liner and do well at getting rid of fresh marks.

In contrast, if your pool liner stain is large or has been present for some time, you will need to invest in a more sturdy and harsh bristle head. Stainless steel bristles are a solid option for this type of brush, as they’ll get to town on those harsh stains that refuse to come out! 

5. Create a Pool Future Cleaning Schedule 

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By the time the four previously mentioned steps are complete, you will be back to a clean and relaxing pool area with no more pool stain liners.

However, there is still work to do! You’ll want to maintain your pool’s cleanliness so that future stains aren’t as likely to occur. 

With that in mind, you’ll need to follow the three steps of a swimming pool cleaning routine: skimming leaves and debris, brushing accumulation from the bottom of the pool, and vacuuming the pool. 

It is worth mentioning that some pool liner stains will happen regardless of how often you clean.

Still, doing proper maintenance can at least minimize the problem and even help you catch the early warning signs of a pool liner stain appearing. Once you see evidence of unsightly marks, do your best and treat the stain as soon as possible. 


Do you still have questions about pool liner stains and how to treat them? We’ve got the answers! 

What is the most common metal that stains pool liners? 

If a stain is in the metal category, iron is the most likely cause. Iron is easy to spot with its red and brown colors. The presence of iron can come from corroding water pipes. Another possibility is that you have corroding pool accessories. Often, a rusted pool ladder will be the culprit of a metal pool liner stain. 

Do pool liner stains decrease the value of my pool? 

For many people, pools should look as well as they function. In that context, pool liner stains can decrease the value of your pool, making treatments even more essential. In fact, if you have an unsightly pool, you could even see your property’s overall value adversely affected.

Why should I wait to swim after a pool shock treatment? 

Besides learning how to clean pool liner stains, you also need to know how to stay safe when doing it. Pool shock treatments contain numerous strong chemicals. With these ingredients, pool shock treatments rid the pool of harmful pathogens and keep it clean. 

However, going into a pool too soon after this pool shock treatment can result in serious health concerns. Common effects include irritated eyes and lung distress. 

More FAQs

Can pool stains be removed?

Pool stains can be removed, but the ease of removal depends on the type of stain. Organic stains are the easiest to remove, and they can be effectively eliminated by shocking or super-chlorinating the pool. On the other hand, metal pool stains are more difficult to remove and require treatment with specific chemicals. It’s important to note that chlorine alone is not effective in removing metal stains.

Can chlorine bleach a pool liner?

Chlorine can bleach a pool liner and cause it to deteriorate rapidly if used in high concentrations, leading to the liner “alligatoring” and the vinyl breaking down.

What causes brown stains on bottom of pool?

Brown stains on the bottom of a pool can be caused by various factors. One possible reason for these stains is the presence of dirty water. If the pool’s filter is not regularly maintained, it can contribute to the development of brown stains on the pool’s surface. Additionally, overfeeding pets or wildlife near the pool and poor swimming conditions can also play a role in the appearance of brown stains on the pool’s bottom.

Will muriatic acid damage a vinyl pool liner?

Muriatic acid can damage a vinyl pool liner if used in large, single doses to adjust pH or total alkalinity levels. The acid is not adequately mixed with the pool water, which can result in chemical attacks on the liner’s printed pattern.

What is the black brown stain on my pool liner?

The black brown stain on your pool liner is caused by the precipitation of oxides. These stains are usually black, but they can also appear as gray or brown, and sometimes even rust-colored. The copper oxides, which can originate from the fittings, are often the culprit. To confirm that you are indeed dealing with metal oxides, it is recommended to conduct a quick test.

What are the white spots on the bottom of my pool liner?

The white spots on the bottom of your pool liner are most likely caused by calcium scaling, which is a result of imbalanced calcium levels and pH in the pool. However, there is no need to worry as calcium scaling can be easily prevented by regularly testing and balancing the water in your pool.

How do I get brown algae stains off my pool liner?

To remove brown algae stains from your pool liner, you can effectively eliminate mustard algae and most yellow/brown algae by directly applying chlorine onto the discolored areas. Use a brush to scrub the stains, and you will witness them vanish. Conduct a water test to identify any other substances present in the water, and treat them accordingly.

Why is my pool liner stained brown?

Your pool liner may be stained brown due to two main types of vinyl pool liner stains. Organic stains, which are typically brown or green in color, are caused by various organic matter such as dirt, leaves, algae, bugs, and other debris. On the other hand, metal stains can result in a range of colors and may be caused by pool ladders, pipes, heaters, or even the pool water itself.

What is the dark stain on the bottom of my pool liner?

The dark stain on the bottom of your pool liner may be caused by the introduction of copper, iron, and manganese from the source water. These elements can react with chlorinated pool water, forming oxides that can then precipitate and leave behind black, brown, or gray stains on the pool liner.

What removes brown algae?

Frequent water changes are an effective method for eliminating brown algae. By performing regular water changes, you can eliminate the nitrates and phosphates that serve as a food source for brown algae. It is important to thoroughly clean the substrate using a gravel vacuum to remove fish waste that accumulates on the tank floor and sinks into the gravel.

Will bleach get rid of brown algae?

Bleach can effectively eliminate brown algae from tank decorations. To do so, you can soak the decorations in a bleach solution every few weeks. However, it is crucial to rinse them thoroughly with water or soak them in water for a few hours afterward to neutralize the bleach before returning them to the tank. Additionally, having algae eaters in the tank can also help control the growth of brown algae.

What is the best thing to clean a pool liner with?

The best way to clean a pool liner is by using white vinegar, baking soda, or organic dish soap. These alternatives are effective in removing mildew and stains, while also being more environmentally friendly and cost-effective compared to other pool cleaners. It is important to exercise caution when using any cleaner to prevent bleaching or fading of the liner.

Can I use Simple Green to clean pool liner?

You can use Simple Green to clean pool liners. It effectively eliminates stains and stubborn residue, and with some effort, it can even remove minor rust. Additionally, Simple Green is safe to use on delicate surfaces like pool covers, plastic pool toys, and vinyl liners.

What are the black stains on my vinyl pool liner?

The black stains on your vinyl pool liner are most likely caused by bacteria that resides in the ground beneath your pool, which can appear years after the pool has been installed.

How do I get yellow stains off my pool liner?

To remove yellow stains from your pool liner, you can dissolve them by using highly chlorinated water. One way to do this is by raising the water level above the stains and shock chlorinating the swimming pool water.

Can you use muriatic acid to clean pool liner?

Using muriatic acid to clean a pool liner should be avoided as it can cause damage to the print pattern on the liner. Instead, muriatic acid should only be used for reducing total alkalinity, as a significant amount of the acid is used up during this process. It is also important to refrain from using any abrasive cleaning agents or aids when caring for the pool seasonally.

Can I use magic eraser on pool liner?

You can rephrase the answer as follows: Yes, you can use a magic eraser on a pool liner without the need for scrubbing. As the season revolves around “hot girl summer,” we are more focused on having a clean girl summer.

Will baking soda remove stains from a pool liner?

Baking soda can be used to remove stains from a pool liner, along with a bleach and water solution. Additionally, there are specific cleaners available for pool liners. To find out more about these cleaning agents, you can get in touch with Kayden Manufacturing. It is important to avoid scrubbing too forcefully while cleaning.

How do you get stains out of a pool liner without draining it?

To get stains out of a pool liner without draining it, you can consider using a metal stain remover specifically designed for vinyl liners. Additionally, employing a stain-removing tool can be helpful. You have the option to directly wipe the stain using a clean cloth or utilize a brush or another liner cleaning tool to access difficult-to-reach areas.

Can you power wash a vinyl pool liner?

You cannot power wash a vinyl pool liner as it is not strong enough to withstand the pressure of a pressure washer. Instead, vinyl pool liners should be cleaned using chemical treatments or non-abrasive methods.

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