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 vinyl liner pool.

Aboveground 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. Your local pool store may be able to test your water for iron, manganese or copper. We have copper test strips available in our pool 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, or 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 — 28 Comments

  1. 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.

  2. 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.

  3. 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…

  4. 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!

Leave a Reply

Your email address will not be published. Required fields are marked *