Causes of Yellow Stains in Toilet Bowl+How to Remove & Prevent

While yellow discoloration in the toilet bowl bottom and walls may be harmless, it can be unsightly and difficult to remove if left untreated. The stains have a hue of yellow ranging from tanned porcelain, faint tint, or a dark golden yellow color resembling ginger.

Yellow stains in a toilet bowl are usually caused by the buildup of minerals in the water supply. The presence of bacteria, the use of certain cleaning products, the age of your toilet, urine stains, tannins rust, and some medications can also contribute to yellow stains in a toilet.

To remove yellow stains from the bowl, use DIY solutions such as vinegar or baking soda, or toilet bowl cleaners that specifically target mineral buildup and bacteria. Regularly cleaning and disinfecting your bowl as well as using a water softener can prevent the stains.

Below are details on the causes and what you can do to get rid of these stains plus tips to prevent them from appearing.

What Causes Yellow Stains in the Toilet Bowl?

Following are some of the most common reasons your toilet bowl has yellow stains

Mineral Build-up from Hard Water

Hard water has a high concentration of minerals like calcium and magnesium. If not treated in time, these minerals can leave behind deposits that pile up over time to form the yellow discoloration in the toilet bowl.

Hard water is also known to cause limescale buildup, which can make stains more prominent.

Urine Stains

Pale yellow stains in your toilet bowl are a result of urine residue accumulation. This is especially common in households with male residents, as they tend to splash more when using the toilet.

Urine has a yellow pigment known as urobilin or urochrome, which gives it its yellow hue. The waste in urine contains phosphorus, potassium, sodium, calcium, and magnesium which produce brown or yellow stains in the toilet bowl known as urine scale.

Some medications can cause urine to turn a darker color, which can lead to yellow stains in the toilet bowl.

Every time you pee, the bowl holds on to the pigmentation for as long as the toilet is not flushed immediately.

Yellow stains in toilet bowl

The more the urine stays the more the color of the stain will intensify. As the surface of the bowl dries, the pigment will etch more causing the stain time even darken after some time.

Further Reading


Another cause of yellow discoloration in the toilet is the tannin available in the water. Tannin is made up of organic matter that is dead and decayed.

Because they are difficult to filter, they will find a way to your water tank, and every time you flush, the water will release tannin that sticks in the walls of the toilet bowl, further causing discoloration.


If you have old pipes and plumbing fixtures, they can release rust(iron) and manganese particles into the water supply.

These particles, through the chemical process of oxidation, can turn not only the bowl but also the water yellow over time.

Oxidation occurs when oxygen reacts with manganese or iron, both metals found naturally in groundwater and soil.


the presence of living microorganisms such as bacteria can also contribute to yellow stains in a toilet. Bacteria that thrive in moist and warm environments, such as those found in the toilet bowl, can produce pigments that create yellow or brown discoloration.

Cleaning Products

Certain cleaning products can cause yellow stains in the toilet. Some cleaning agents such as bleach can react with the minerals in the water or with other chemicals present in the toilet bowl resulting in yellow or brown stains.

Age of the Toilet

As a toilet age, the enamel or glaze on the surface can wear down or become damaged, making it more susceptible to staining.

How to Remove Yellow Stains from Toilet Bowl Bottom and Walls

Now that you know what is causing the stains , let’s look at different ways you can get yellow stains out of your toilet bowl bottom and walls.


Remember to follow all safety precautions when using any of the bowl cleaning products. At all times test a small, inconspicuous area first to avoid damaging the toilet bowl.
Use personal protective equipment such as latex gloves to protect your hands from dirt and germs while cleaning and safety goggles to cover your eyes while spraying and wiping chemicals


Vinegar is acidic in nature, therefore, offers the right chemical solution to getting rid of the stains. If the extent of the pigmentation is not severe, using this acidic solution is the perfect choice for removing these stains. Remember to wear rubber gloves to protect your hands.

Cleaning Vinegar
Calyptus Vinegar


  1. Take a cup of vinegar and pour it generously into the toilet bowl making sure all the areas of the bowl are attended to.
  2. Let it sit for a while to dislodge the yellow stains.
  3. Scrub gently with a brush or a sponge.

This method is rather easy and straightforward as you only need to let the vinegar work its magic. For a more reactive approach, you can warm up or heat the vinegar to a good temperature then pour it into the toilet bowl. Use a strong scrubbing brush.

The most common problem with vinegar is the smell it leaves behind. The solution is to get cleaning vinegar that is infused with organic flavors that will leave your bathroom fresh and spotless

Coke and Baking Soda

Coke contains phosphoric, carbonic, and citric acid which work very well with other acidic materials. Mixing these two options is the best solution for tougher stains.

You could also add a pinch of sodium bicarbonate to take things up a notch. The mixture will double up as a bleaching solution as well as a disinfectant.


  1. Pour two cups of Coke and pour it into the toilet bowl.
  2. Open the box of baking soda and sprinkle it in the bowl as well.
  3. Leave for the effect to take place.
  4. Come back and scrub to remove the yellow pigmentation.
  5. Rinse it up. with clean warm water

Baking Soda and Vinegar

A mixture of baking soda and vinegar generates a chemical compound called carbonic acid, which is aggressive on stains and mineral deposits on surfaces. It will be an excellent remedy for this problem.

Baking Soda
Baking soda


  1. Measure about a cup of vinegar and pour it inside the toilet bowl. Swish it around so it gets to every area in the bowl.
  2. Let it sink in the bowl for about half an hour to one hour.
  3. After that time, open the box of baking soda and sprinkle it all over the toilet. The vinegar you added previously will ensure it sticks on the walls of the bowl.
  4. Add some vinegar to activate a fizzy reaction.
  5. Let it fizz for another 15 minutes, then come back and brush the interior surface of the toilet bowl.
  6. Scrub the toilet with nylon stifle brush and rinse off by flushing. The toilet should be stain-free.

You can repeat this method as many times as possible. You could even leave the solution overnight to let it work through the tougher stains. 

Borax and Vinegar

Borax is also an excellent multipurpose cleaning, especially on really tough stains. A mixture with vinegar only makes it better.


  1. Add about a cup of borax into the toilet bowl.
  2. Add some vinegar right over the borax.
  3. Gently scrub the toilet. Let sit for 15 minutes and flush the loo as you scrub again.

Borax Paste

For those deep yellow/ golden stains, a borax paste should do the trick. Here’s how you can do that;


  1. Wipe down the toilet bowl to get a clear view of where the mold is.
  2. Make a paste in a dish using borax and water. Ensure the paste is thick enough to stick on the walls of the bowl.
  3. Apply the paste over the hard-stained areas and scrub gently with the hand brush to make sure the paste is all over the bowl.
  4. Leave it on for half an hour.
  5. Once back, scrub again gently to scrape off the brown stains.
  6. Flush the toilet to finish up.

You can replace the water with vinegar in case you want a more reactive solution. Just ensure you add only a little amount so the borax can still mount on the wall

Automatic Toilet Cleaners

There’s always a fast and easy way to get things done without looking for home DIY methods to clean the toilet. Simply head to the store and look for the toughest toilet cleaner.

A good recommendation is CLR PRO multipurpose cleaner. It is an EPA-certified non-toxic calicium, lime and rust remover designed for bathrooms or bathroom related surfaces.
It quickly removes calcium, lime and hard water deposits, soap scum, discoloration and dirt leaving behind a streak-free shine.

Mineral deposit remover for toilet bowl

Use Pumice Stone

This method is the best for stubborn yellow stains.

  1. Wet the pumice stone
  2. Gently scrub the stains on the toilet bowl.
  3. Be sure to keep the stone wet while scrubbing to avoid scratching the surface of the bowl.
Pumice stone toilet bowl for stubborn stains
Powerhouse pumice stone

How to Prevent

There are several measures you can take to prevent yellow stains from etching in your toilet bowl. Here are some ways to avoid the stains.

  • Use chlorinated tablets to keep the toilet clean and free from urine pigmentation.
  • Maintain a cleaning routine as regularly as possible to ensure the pigments can’t etch in the Porcelain. Constant cleaning and leaving of disinfectants overnight will kill any likelihood of the stain forming.
  • Always flush the toilet after use whether it’s a short or long call. Also, remember to clean the guest bathroom and flush your toilet daily even when not in use.
  • Avoid using aggressive measures to clean the toilet because tools such as the pumice stone can cause cracks or dents in the toilet bowl. So when the urine starts to pigment the walls, you can’t reach the crevices to clean it out.
  • Use a water softener or a filter on the water supply to reduce mineral buildup. Carbon filtration can aid in getting rid of tannins from the water. Adding the filter can save you the extra work of cleaning up.
  • Regularly disinfect the toilet bowl and seat.

More on Toilet Cleaning


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