Stains and Discoloration in a Vinyl Liner Pool


When your pool and backyard is as post card pretty as this pool, the last thing you want are stains on your pool’s vinyl liner.

Above ground or inground pools both use vinyl liners, and are susceptible to staining from minerals, organic materials and chemical damage.

For all of you vinyl liner pool owners, here’s how to identify, treat and prevent staining of your vinyl liner pool.


One advantage of vinyl pool liners is that the slick surface often reduces mineral staining. It’s not uncommon to see the pool stains more pronounced on plastic and metal items in the pool, such as on your ladders, steps and pool lights.

Vinyl liners also can stain in localized areas or spread throughout the pool surfaces. It can be just one small spot or only at the waterline, on on the pool steps. Size, color, location and any “behavior” of the pool stain can be helpful in identifying the source or cause of the stains.

copper-test-stripsTesting your pool water for mineral content can also be helpful to identify pool stains. Test your water for iron, manganese or copper. carries copper test strips available in our water test kit department.

Mineral Pool Stains

Mineral pool stains can be every color of the rainbow, but a few are more common. Blue/Green stains are usually from too much copper in the water. Iron pool staining can be brown, red or a yellow / orange color. Calcium or sodium salts can leave whitish deposits on your pool liner.

For stains on a horizontal surface, you can test the surface for mineral staining by using a small amount of acid on the stain. Place a vitamin C tablet (ascorbic acid) on the stain for a short time period. You can also use pH decreaser (sodium bisulfate) placed into a sock. If the stain lightens considerably, you have a mineral stain on your hands.

Organic Pool Stains

Organic stains come from dead algae, or other small animals, or from the tannins contained in leaves and plant debris. Organic stains can stain a range of colors from yellow to brown to black. These stains normally occur after a long winter or after a big thunderstorm.

Organic chemicals respond to chlorine applied directly on the surface. Sometimes just shocking the pool will lighten or remove organic pool staining. Place a chlorine tablet on a stained area for just a few minutes. If the stain lightens, then you have an organic pool stain.

Chemical Damage

Fading can occur from the sun naturally over time, or vinyl liners can become “bleached” from high chlorine or low pH levels. Broadcasting granular chemicals into a vinyl liner pool is generally a no-no, instead pre-dissolve into a bucket of water first. Chemical or UV damage is not considered a stain on the pool surface and is generally not treatable.

jacks magic stain-ID kit helps you determine which steps to take next to remove your pool stainsUnsure of which type of vinyl pool stain you have? The Jack’s Magic Stain ID kit helps you determine what the next best steps would be to remove your particular type of pool stain.


To begin treating a pool stain, the first step to take (after identification) is to balance your pool water chemistry. In some cases, merely adjusting the pH, Alkalinity and Calcium Hardness levels can lighten or remove some types of pool stains. Use a fresh pool test kit or test strips, and adjust your pH to 7.5 – Alkalinity to 100 – and Calcium Hardness to 200.

Mineral Pool Stainspool chemicals for stain removal and prevention

Generally speaking, mineral pool stains respond best to a treatment with acids. Plaster pools may be acid washed, or a stain-master used for localized rust stains – but you can’t acid wash a vinyl liner pool, can you?

Vinyl pool stains can be removed with acidic stain removal products like Stain Free, or A+ Stain Remover, or Jack’s Magic Blue Stuff for vinyl liners. If the stain is on your vinyl pool steps, try Jack’s Magic Step Stuff.

Organic Pool Stains

Generally speaking, organic pool stains respond best to a treatment with oxidizers. For plastered pools, you can just dump powdered shock right onto the bio-stain, and watch it instantly disappear, but you can’t do that with a vinyl liner pool, can you?

Organic pool stains can deposit themselves only around the main drain, on the steps or corners of the pool. Balance the chemistry, add super pool shock, according to directions. If that doesn’t remove the organic stains, try one of the products listed above. Safe for vinyl liners, and they work for both mineral and organic pool stains.


Keeping your pool water balanced and the pool clean, especially during the off-season, is important for keeping your pool stain free. If your pool water comes from a well, it may contain high metals and minerals. And of course, always use stainless steel screws on your ladders, lights, steps and faceplates – and ban the use of hair ‘bobby pins’ in the pool.vinyl-pool-stain-prevention-chemicals

To control pool stains from metals and minerals, use Jack’s Magic Purple Stuff or MetalFree. Our own Super Stain Away is very popular, and for severe mineral and metal issues, CuLator will reduce levels.

These stain prevention pool chemicals control pool staining by making it difficult for minerals in the water to precipitate out of solution, where it can stain your vinyl liner, steps or ladders.

No one likes stains in their vinyl pool! If you have been battling pool stains, and are finding it difficult to resolve, give our pool stain experts a call here at 800-288-7946!



Davy Merino
InTheSwim Blog Editor


Stains and Discoloration in a Vinyl Liner Pool — 57 Comments

  1. I had my concrete cleaned and sealed around pool. The sealer got on the top of vinyl liner. How can I clean this. It is rough and tacky.

    • Hi Fisher, start with a degreaser, like Simple Green, spray it on and rub gently with a textured sponge. If that does not respond, you could ‘verge’ into acids or solvents. Most sealers will respond to xylene or acetone solvents, but you can imagine what these do to liner patterns, can just melt them off. If degreasers don’t work, Try scrubbing with baking soda and a stiff brush, or you could try a mild acid like vinegar, or …you could try dabbing on a solvent, being careful not to spill it, or rub too hard. If nothing works, I suppose you may have to try to live with it…?

  2. I have developed a re-0ccurring yellowish stain pattern in the same area all summer long.
    I’ve used super algicide, high chloride shocks, with no effect.
    I’ve used metal removers of many different brands, no effect.
    The only thing that removes the stain is the A+ Stain Remover. But the stain returns in three days.
    I’ve used the drop in packet for the filter basket, no effect.
    It’s a inground vinyl 22 x 44.

    • Hi Vince, OK, so the ascorbic acid (A+) removes it but only temporarily. Stains like behave that are often on the underside of the liner, on the floor, or something on the wall. These are of course nearly impossible to remove, without pulling up the liner. Another yellowish stain that possibly could behave like this is a chlorine burn, if a tablet sits on the vinyl, in which case the vinyl is usually discolored, more or less permanently. I’d probably suggest continuing to treat with A+, perhaps several treatments could fix it.

  3. Hello! I need your help please. The pH levels have been very low, so I added 5 lbs at a time over several days (as per the pool store instruction). The levels have finally come up. There was a very bad storm that moved thru last week. I thought there was dirt on the bottom of the pool but I have brown stains on the bottom of my new liner! They look like theyre spreading.

    Any advice you can give me would be greatly appreciated.

    Thank you!

    • Hi, not sure what the brown stain could be, but could be a mixture of scale and dirt, or some metallic stain like Iron. I would start by doulble checking pH, alkalinity and calcium hardness levels, and then use our EZ Stain Remover product according to directions, or our A+ stain remover – both will target specific stains, hard to say which one will work best, try EZ first, with fingers crossed, and if it doesn’t work well, try the A+. Just pour in following directions, and brush the pool well.

  4. Hello, we are just getting around to opening our pool this season. It was full of leaves and algae. We drained the pool and scrubbed the sides. All of the brownish color and algae came off very easily, but there’s a white scale that’s still on the entire liner. It comes off if you gently scratch at it with your fingernail, but the pool is 18×30, so that would take forever. What would you recommend that is a gentle cleaner for the liner. Again, the pool is empty right now.
    Thank you:)

    • Hi Sunny, if it is a scale, I would try using some vinegar, diluted 50/50 with water. In a spray bottle. Simple Green is another chemical, for another purpose than scale, for grease. Since you’ve cleaned the pool already, try spraying or wiping on a mild acid like diluted vinegar or lemon juice to see how that does on the scale

  5. I have used your super stain remover and it took care of the stain on the bottom of the pool. We have brownish/yellow on the walls we also had a problem with phosphate problem covering the entire pool used phos free and took care of that problem the walls and the skimmer basket in side is brown do I have a metal problem and what can be done for the walls.


    • Hi Robert, Stain Away and Super Stain Away and other sequestering agents keep minerals and metals in solution, by molecular bonds. these bonds become weak with chlorine and sun exposure, and higher water temperatures, etc. Maintenance doses every 2 weeks works well for most folks to replace what has degraded. Be sure water is very well balanced, (Ph, Alkalinity, Calcium) and add more Sequestering agent to see if it will re-dissolve the existing stains, back into solution, if you are lucky. Walls can be harder to treat with our stain removers like EZ Stain and A+, because they are on a vertical surface… so first be sure water is very well balanced, and brush the walls several times per day. If they don’t come clean, you can treat with a stain remover by pouring down the walls, and using your brush… but not very effective. You could add several pounds into a tube sock and create a stain bag, to rub on the worst areas, that sometimes works well.

  6. I have a 24 ft above ground pool vinyl liner and keep getting metal stains…I have lowered cl to 0 multiple times…ha e used stain away and a+ stain and seaklear and vit C and oxalic acid and used the pool store chelator and metal free..pretty much done it all! I can get the stains lifted but will NOT chelate for long even adding chelator every 2 weeks as suggested. I am about to give up…water is perfect on all levels otherwise…I even used a culator and it didnt do much…thinking of plain citric acid to lift and no clue what to chelate now…tried it all

    • Hi Chris, sequestering agents (chelators) have a short life in the pool, they degrade with sun and chlorine in 1-2 weeks. Shocking can destroy the bonds created, and precipitate metals. Have you tried slightly larger doses, or adding weekly maintenance doses? Just more of the same thing? We have many chelators, (Stain Away, Super Stain Away, Metal Free, Metal Clear, Metal Sequester, and Jack’s The Blue Stuff). You could also start using a pre-filter on the hose that adds water to the pool, possibly replacing a portion of the water, if metal content gets really high.

  7. Hi! Every time I get my PH and acid levels up, my chlorine drops- I shock it and I get dark staining in various areas. I used some ascorbic acid and it looks great again but I get pink algae. Then I shock to get rid of it and I am back to square one with low numbers, HELP!

    • Hi, chlorine works best at low pH levels of 7.2-7.4, when it gets higher, chlorine gets sluggish. How’s your cyanuric acid level (stabilizer)? Too low and the sun burns it off too quickly, and too high and again chlorine is sluggish and slow to react. The staining from shocking may be lots of metals (iron/copper/silver) in the water. Using a sequestering agent like Stain Away can help prevent that from happening. Pink Algae is a form of bacteria that can hide from chlorine very well, and remain dormant until levels are low. It may be hiding in your filter or in some soft materials like fabrics and foams used in the pool (nets, bags, brushes, swim suits, filter media).

  8. I have a new vinyl liner one year old. I just noticed a one ing by one inch small spot that has lost color. Is there anything I can do to “recolor” this spot?

    • Interesting question – if you saved any of the cutouts from the liner install, you could cut a patch of the same size, and glue it down. It may be possible to darken the vinyl, with some dye, but you’d have to drain the pool to do so, and I’m not sure what type of dye you would use, but there is likely something available online, some vinyl dye or colorant.

  9. I have been battling green algae for several weeks. I have used several algaecides and a back and forth of chemicals to get the water balanced. finally got everything working in concert but the bottom of the above ground pool liner is discolored in a yellowish green hue. Where should I start?

    • Hi, start with perfect water balance, pH 7.4-7.6, Alk 80-120, Cal 200+ – and then I’d probably try to use regular cal hypo, 65% strength, shock the pool with 2 lbs per 10K gals, then brush with a good pool brush, very vigorously. Run the filter, and vacuum to waste if possible, the shock dust or residue. Keep running the filter long hours for now, it will help. If the shock does not remove the stain, I’d go with an acid, either ascorbic acid in StainFree or our A+ Stain Remover, or our EZ Stain Remover products

    • Hi Karen, those are probably metal stains, possibly from overuse of copper algaecide, or from well water, or old metal pipes. Keep using metal remover, weekly, to keep minerals and metals in solution, and be careful when shocking the pool (use low doses with a low pH), to keep the metals from dropping out of solution, from a heavy shock treatment.

  10. I’m confused. I’m trying to find something that will work on our unground pool with a vinyl liner. Last year there was a chemical reaction … iron … that stained our whole pool orange. This year it is still there just less orange and not the whole pool. I’ve done the test with Magic Jack’s and it is definitely iron. The confusion is which Magic Jack’s product should I use? Thanks for your help.

  11. I have an above ground pool with a vinyl liner. Last season we noticed a brownish colored stain near the bottom drains of the pool. When we shocked the pool the stains would completely disappear.
    This season the discoloration is much larger and does not disappear when we shock the pool. We’ve taken water samples to the pool store. First diagnosis was black algae. We treated it with algaecide. No change. The another water sample in and this time showed signs of copper in the pool. So we treated it with a metal out chemical. No change. We’ve heard now that it’s possible the stain is caused by a mold underneath the liner that is showing thru a lightened blue liner. Have you heard of this. Is there a fix in the short term without having to remove the liner completely and treat the ground under the liner??

    • Hi Brent, I have heard of mold under the liner. One treatment is to inject bleach through tiny holes in the liner, and then patch the hole with Flexible Sealer or EZ Patch 28. If you had a nifty rig to dispense the bleach, like a long hospital IV type deal, you could perhaps do this without draining the pool (?) Sometimes, (like last year perhaps) sprinkling shock and/or bleach over the area can bleach the area, from the poolside. You could also try Ascorbic Acid, or A+ Stain remover, to see how that does when sprinkled over the area or used in a stain sock. Stain socks can also be made with pH decreaser or EZ Stain Remover, both mild acids.

  12. I have stains throughout the bottom of my pool. I have an above ground 21′ round pool with vinyl liner. I tried the vitamin C tablet and didn’t have any lightening. I tried lowering the pH level, then adding a Stain Lift chemical, but that didn’t lighten it. I tried scrubbing with a brush, a sponge – nothing. I tried a Mr. Clean Magic Eraser, and that helped a little bit, but also had trouble with it dissolving in the water. The pool water is crystal clear and the I keep the pool very clean. I have no idea where these stains are coming from and how to get rid of them. Help!

    • Hi Theresa, you didn’t mention if you used a stain & scale chemical (sequestering agent), which is used to lock-up minerals and metals in solution. MetalFree, Stain Away, or Jack’s Vinyl Liner Blue Stuff, would be good choices. In some cases, they can dissolve existing stains from metals and minerals (scale), and regular treatment every few weeks can keep them in solution. Another treatment, completely separate from what I just mentioned, is to shock the pool quite heavily, with 2-3 lbs of shock, per 10000 gallons, which will not remove mineral/metal stains, but is very effective on organic stains from debris/dirt or algae remains.

  13. I have had a 15′ aboveground pool for 25 years. This one I have had for 3 years. I always broadcast a pound of shock every week or week and 1/2. I always keep the pump running. I have never had a problem until a week ago. 3/4 of my liner is white. I had been using Clorox pool and spa xtra blue chlorinating granules. People were in the pool several hours after shocking and the next day. That night I was in the pool and was shocked that the liner had turned white. I have turned in a claim to the company. Any other suggestions?

    • Hi Cindy, when adding granular chlorine (shock) in a vinyl pool, pre-dissolving is always indicated, to prevent bleaching of vinyl liners. It’s probable that your old liner was just more resistant to the chlorine, whereas the new one has lost it’s pigment rather easily. Check the label on the Clorox, probably says to pre-dissolve, in the fine print…

  14. I have an in ground pool with a vinyl liner. When we first opened it, it was a pond! Over the last week and a half, we’ve added about 60 gallons of shock, but on the first round, I had added 4 gallons of algaecide. I’ve learned that was probably a bad thing to do. Now, I have a copper/orange stain all around the pool. From reading the internet, the algaecide probably had copper in it and has caused this staining. I threw away the bottles, so I really don’t know if they had copper, but they probably did based on the discoloration of the pool. So, once I finally get the water clear, how do I remove that staining that is around the permiter of the pool and on the sides of the steps. The steps are fiberglass. One more thing. I need this looking good in 5 days! Can you help?

    • Hi Amanda. First thing to do is to keep it filtering as much as possible and test the water every day, so you have the best possible water balance. Then add a stain & scale chemical like Super Stain Away, a sequestering agent, to try and reabsorb the metal into solution. If that doesn’t work well enough, use an acidic stain remover, like A+ stain remover, or use EZ stain remover, either sprinkling over stains, or for more localized stains, put 1 lb of the granular in an old sock and slowly move it around the wall stain, dragging it with your pool brush. jacks magic also makes the Step Stuff, made specifically for vinyl liner steps. Good luck – 5 days is not much time!

  15. yes, good day, I opened my pool 2 weeks ago an took a sample to the local pool supply store an everything was ok calcium was just a little low an added 5 lb. cal. increaser, so this week I was doing my weekly maintaining vacuuming an shocking, I noticed a stain in the deep end an tried to scrub but didn’t come up, A few days before I added a bottle of the 90 day algaecide in which half one day an half next day, what do I need to do an what caused this the 90 day algaecide

    • Hi Will, Seaklear 90 day is a copper based, but at 3% one of the lowest. Copper staining could occur from overuse of copper algaecides in a plaster pool, without using a stain & scale chemical, but i doubt that one treatment could create a localized stain like you have, especially if you have a liner. First thing is to double check all water balance measures, and you could make a stain sock with A+ stain remover, or use EZ stain remover, by placing 1 lb of the granular in an old sock and slowly moving it around the stain with your pool brush. Finally a use for those orphan socks!

  16. Davy
    I have a pool with a vinyl liner and fiberglass steps. I opened it last week and it contained a good bit of green algae. I’m currently shocking it to remove the algae but now the pool has brown staining on the steps, skimmer, and liner.
    I’ve had the pool for about 25 years and never had this staining. I’ve tried scrubbing it but it will not come off. What products should I buy to remove it? Thanks

    • First thing is to balance the chemistry, with proper levels of alkalinity, calcium and cyanuric acid. Then adjust the pH down to the low end of the range, 7.2-ish. Keep the chlorine level above 2 ppm consistently, and run the pump overtime, 18 hrs+ per day. Take your time with this, and give the water a week to adjust, and absorb sunlight, and filter. Speaking of the filter, make sure its in top condition, cleaning or replacing the filter media if needed, now may be a good time. Once things have stabilized for a week or so, then begin the stain removal process. First thing to try would be a stain & scale treatment, like Super Stain Away, just follow label instructions. It’s a sequestering agent for metals and minerals, to keep them locked up in solution. If that doesn’t do much, after a week or so, double check all water balance measures, go with some mild use of an acidic stain remover like A+ stain remover, or use EZ stain remover, either sprinkling over stains, or for more localized stains, put 1 lb of the granular in an old sock and slowly move it around the stain with your pool brush. Finally a use for those orphan socks! Good water balance, chlorine levels and filtration is also important!

  17. Hi. Just opened inground, vinyl liner pool. Chemicals are balanced and water is clear. But have a dark stain around the perimeter of the main drain in the deep end. Not sure of the exact color but it’s dark and looks horrible. Any recommendations on how to determine the cause and then recommendations to get it clean? Thanks,

    • Hi, usually that’s from worms, or other debris laying there all winter. You can use chlorine – powdered pool shock put into a tube sock or nylon sock, tied off and then pushed down with your pool brush, held over the stain, and pushed around slowly. If that doesn’t work, you can do the same thing with pH decreaser (sodium bisulfate). Stain Free can also be used (ascorbic acid).

  18. I have an inground salt water pool with a vinyl liner. There are unremovable light brownish/greenish stains around the perimeter on the bottom. When I place my solar cover on the pool, the stains disappear as if they never existed. When I take my cover off to use the pool, and after a few hours of sun exposure, the stains reappear. Help.

    • I have never heard that one before! They reappear with sun exposure? Photoactive substances, is that the right word? Interesting, but i don’t know what that would be!

  19. Hi, I have an Endless Pool with a vinyl liner. Almost the entire bottom has a greenish yellow stain that is gritty to the touch. It does not scrub off. I think it is dead algae stain. Anyway I am draining the pool. Not sure if I should drain all the water out since I have heard of popup. Then I was going to add a lot of chlorine to see if that would bleach the stain. I just read your tablet idea. Wish I had read that before:/ The Endless pool support person recommended Wipe Out. Please tell me what you recommend.

    • Hi, if it is gritty and won’t brush off, that leads me to believe that it may be calcium nodules or crystalline deposits of minerals, mixed with dirt, algae, etc. High calcium hardness levels combined with high pH, can cause minerals to scale and deposit on surfaces. If that seems plausible, I would try a sequestering agent like Stain Away or Scale Free, to dissolve and absorb the minerals back into solultion (be sure to balance chemistry – ph, alk, calcium, chlorine first). If that doesn’t work, I’d next try StainFree, and ascorbic acid, in an attempt to dissolve the stuff, brush it up, and vacuum it away.

  20. Hi Davy,
    When we opened our pool about a week ago, we found that our beautiful vinyl pool liner has some significant staining from leaves and acorns that settled over the winter. I was able to rub a chlorine tablet on the step area and a few of the heavy stains came off, but I can’t reach the liner in the deeper areas. Any suggestions?

    • Hi, organic stains such as these respond well to chlorine in most cases, as you’ve discovered. With plaster pools, you just sprinkle some shock over the area, let it sit for a few minutes, and voila (mostly) gone. Vinyl pools, well you aren’t supposed to sprinkle cal hypo shock, and have any non-dissolved granules in contact with the liner but… you could do a test with shock, pouring a cup or so over the area, let it sit for a minute, then brush the area well. You need the regular pool shock (Cal Hypo), not the quick dissolve stuff, or the non-chlorine stuff normally used in vinyl pools. Also be sure that your pH is balanced, or in the 7.2-7.4 range, which can also help remove the stain. Another chemical that works well on organic stains is Stain Free, made with Ascorbic Acid, if you don’t want to use pool shock. Third option is to buy a swim mask or goggles, and practice your breath holding! 🙂

  21. Hi Davy. I have a 18 X 36 in ground vinyl liner pool with 4 feet of stairs. Their is this yellow stain on one side of the deep end of the pool. Their is some light yellow strain on the stairs. I was told to rub an lemon to see if the stain came up. I did this with very little change. I test the pool all the time and the levels are ok. What should my next steps be and what chemicals do I need.

    Thank You
    Robert Grande

    • Hi Robert, yellow stains on vinyl and steps can sometimes be from a chlorine floater, did you use one during winter? Chlorine stains can be hard to remove, if so. If not, you could take the lemon test to another level, and use Stain Free (made with ascorbic acid). To test if it works before you buy, you can use crushed up Vitamin C tablets on the area, to see if that removes the stain. You can also use pH decreaser, in a tube sock, as a stain bag, just lay it over the stain, or hold it on the deep end stain with a pool pole.

      • what a chlorine floater can cause rust color stains?, had a above for yrs but this yr 1st time to have this problem, everything has a rust color stain on it, esp anything white pn the water, water is clear, not sure what to try next?

        • yes, trichlor tablets can create a burnt orange color or stain, but only when they sit on the surface of a step or plaster. Wont create an all-over stain. Sounds like Iron or Rust in the water. Check for any sources of corroded metal, and use a stain & scale like Stain Away or Super Stain Away, to try and dissolve the metals back into solution.

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  23. I have an 18ft round above ground pool. About 2 yrs after a new liner was put in, a dark grayish stain began to form from the water line and up about 2-3 inches. It formed around the 3/4’s of the pool and only where the sun hit the liner. It isn’t a specific color, but it looks dirty. I took a picture and went to 2 pool stores and neither recognized it or knew what it was. It doesn’t clean off and even fine steel wool doesn’t get it off?????

    • Hi, wind blown dust and dirt, or pollutants from planes, cars or industry come to mind. I can’t say exactly what it could be – but could be fading of the liner, in a very odd way! Normally they just ‘fade’, but don’t get darker. I’m at a loss to what it is… but it seems like it’s stuck on there pretty good. You could try some vinyl cleaner or mild acids, in a small test area to see if it would work – but you’ve probably done that already…

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