How To Clean Toilet Bowl Stains – 7 Methods

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No one likes cleaning toilets, and it’s even worse when there are hard water stains (or other types) in the toilet bowl that just won’t come off.

These stains look unsightly, and they also make it feel like you haven’t done a good job of cleaning the toilet bowl!

Well, you probably haven’t tried everything just yet. Here are a few ways to clean toilet bowl stains that you might not have tried yet.

woman cleaning toilet bowl stains

How To Clean A Stained Toilet Bowl

You may find that one (or more) of these methods will easily remove those stains in the toilet bowl. Then again, you might not! It’s worth a try, right?

Important Note: It needs to be mentioned that if you have a septic tank, you need to be very careful what actually goes down the toilet. Some of the chemicals and methods listed below will kill the good bacteria in your septic system and that causes all sorts of problems.

1. Toilet Bowl Cleaner Under Flapper

What’s a flapper? Well, the image below will help you with that – follow these instructions to not only to get rid of even the most stubborn stains, but also to give the parts of the toilet you can’t get to a good clean out too – eliminating the source of a lot of future stains.

toilet flush mechanism - flapper
  1. Turn off the water to the tank
  2. Flush and drain the tank and let it dry completely
  3. Pour toilet bowl cleaner under the flapper until it comes out all holes in the bowl (even the front ones)
  4. Give the bowl and the stains a scrub with a toilet brush
  5. Let it sit for 15-20 minutes
  6. Turn the water back on and flush the toilet
  7. Continue flushing until clear water is coming out into the bowl

This should remove most of the stains. If you have some stains leftover then repeat the process with CLR instead of toilet bowl cleaner.

If you want to further protect your toilet from future stains, then consider installing the Kaboom Continuous Clean system. It really does work wonders and doesn’t damage your seals like bleach tablets do.

Best Choice
Kaboom Continuous Clean system

Toilet Bowl Cleaner System


  • One easy-to-install device and two refill pouches
  • Powerful bleach-based formula does all the cleaning
  • Safe on septic systems and all toilet tank parts
  • Keeps your toilet clean for up to six months – three months per pouch
  • No more dirty brushes. No hard scrubbing

2. Muriatic Acid

This method is a bit more extreme, but should help with those really stubborn stains.

For this method, you will need muriatic acid which can be quite dangerous – so make sure you read the label and follow all safety directions.

  1. Open up windows and turn on any exhaust fans
  2. Mix 1 part muriatic acid to 5 parts water
  3. Pour it slowly into the toilet bowl (you don’t want to splash this stuff anywhere)
  4. Fill it only to the normal water level – otherwise, it will go into the sewerage system and that’s bad!
  5. Let it soak for a few hours
  6. Do not flush! You will need to manually scoop out the acid and dispose of it as per the product label
  7. This should soften up or completely remove tough stains in the bowl

3. Lysol Black Label Toilet Cleaner

If you want an off-the-shelf solution, then Lysol black label toilet cleaner is about as good as it gets.

It contains Hydrochloric Acid which directly attacks stains caused by hard water and iron in the water.

  1. Flush the toilet
  2. Squirt the Lysol Black label liquid into the bowl and under the rim – ensuring all surfaces are covered.
  3. Let it soak for at least 10 minutes
  4. Use a toilet brush to scrub the entire bowl surface and then flush
  5. Repeat if required
Best Choice

Toilet Bowl Cleaner


  • Hard water toilet stain-dissolving power
  • Thick formula coats the entire toilet bowl
  • Specially formulated to destroy hard water stains in your toilet
  • Cleans as it disinfects
  • Will not harm plumbing or septic systems

4. With CLR

CLR just has so many uses, doesn’t it? Well, it also can be great for removing stains in your toilet bowl.

  1. Flush the toilet and then let the bowl completely dry. If the stains are below the water level then you will need to turn the water off and completely empty the bowl
  2. Soak some paper towels in CLR
  3. Stick the soaked paper towel to the entire surface of the bowl
  4. Let it sit overnight
  5. In the morning remove the paper towel and give the bowl a scrub

5. Remove Stains With Iron Out

Iron Out is a great stain remover that many people seem to overlook. Don’t do that here, it does a great job in the toilet too.

  1. Spray Iron Out on the stains
  2. Let it sit for 5-10 minutes
  3. Scrub the bowl
Best Choice
Iron out rust stain remover

Rust Stain Remover


  • Powerful gel clings to dissolve rust stains on contact; no scrubbing necessary
  • Quickly and easily removes the toughest rust stains from most surfaces in and around the home
  • Ideal for vertical and hard to reach surfaces, like showers, sinks, tubs and toilets above the water line
  • Versatile liquid formula, great for bathroom, kitchen, colorfast carpet and fabric, tile, concrete and many other interior and exterior surface applications

6. Use a Magic Eraser

Have you tried a magic eraser on the stains? They can do quite a good job and won’t damage your toilet.

Simply use a magic eraser to… erase the stains! It might take a few goes but it can definitely help.

7. Use Coca Cola

What? Coke? Yep – you have probably seen what it does to rust.

But guess what? It can also remove stains from your toilet!

  1. Switch off the water supply to your toilet
  2. Flush the toilet and plug the hole in the bottom with something water proof
  3. Buy 3 x 3 Litre bottles of Coca Cola
  4. Poor them into the toilet bowl up to the rim (so they cover the stains)
  5. Let it sit for a couple of hours at least
  6. Remove the plug and let the coke drain away
  7. Give it a scrub if it needs it – the stains should be easy to remove now, if not gone completely!

Are Your Stains Gone?

So hopefully one of these methods has worked for you and those ugly stains are gone from your toilet!

If you have any other sure-fire ways to remove those pesky toilet bowl stains then comment below!

pinterest toilet bowl stains

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Aaron is the founder of and Essential Home and Garden. With over 15 years of hands-on experience in home ownership, lawn care, and gardening, Aaron is a seasoned expert in areas like lawn care, DIY, HVAC, and pest control.

5 thoughts on “How To Clean Toilet Bowl Stains – 7 Methods”

  1. Avatar photo

    Pour a small amount of muriatic acid into the toilet and let most of it react away or, inevitably, evaporate. It is really strong. What’s left is gets deluted enought that it can be flushed down the sewer. Nobody wants to scoop stuff out of a toilet. Metal parts shouldn’t come into contact with the acid or its vapors. Pipes in and near the toilet tank can rust. Polished metal will tarnish immediately.

  2. Avatar photo

    Is there a solution to remove acid patches from the toilet bowls. The acid spoiled the bowl (Hindware). Please give a reply soon

    • Aaron Green

      Hi Tom, Unfortunately, you have probably damaged the finish of the bowl….the only real fix will be to replace it I think.

  3. Avatar photo

    i can contribute a method that does NOT work but it pops up whenever you search toilet cleaning methods. the Borax-vinegar method. Yes I put Borax on very liberally, yes I swished it around, put the required amount of vinegar in, let it set 1/2 hour before brushing. NO improvement at all!

    • Avatar photo

      I try Borax and vinegar too with no results on my vertical toilet bowl stains and nothing happened.

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