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How To Remove Brown Stains in the Bottom of the Toilet Bowl

If you’ve recently spotted a brown stain at the bottom of your toilet bowl, you may have started to question your hygiene and cleanliness habits. 

Fret not, the stain is most likely caused by hard water. The bad news is that you will need a bit of effort to remove it. 

Unless of course you’ve not scrubbed your toilet in a while, in which case your original suspicion might turn out to be quite correct. 

Here is what you can do to remove the brown stain at the bottom of your toilet bowl:

Pour White Vinegar Into the Bowl 

White vinegar is amazing at descaling kettles and removing limescale from any item whatsoever. 

Pour an entire litre into your toilet and let it sit as long as you possibly can, ideally overnight. To achieve an even better result, drain your toilet bowl first, and give it a good scrub in the morning before flushing the vinegar out. 

Pour Citric Acid Into the Bowl 

Citric acid is more acidic than white vinegar, so it will dissolve limescale even more effectively. 

Bring a kettle of water almost to the boil and add a quarter of a litre of citric acid to it. You don’t have to squeeze actual lemons, you can buy citric acid at the store. 

Pour your mixture into the toilet bowl, let it sit overnight, then give it a good scrub before flushing. If you can, drain the bowl beforehand. 

Combine Citric Acid and Vinegar 

For extra cleaning power, you can also combine the vinegar and citric acid. 

The best part is, you only need a few drops of lemon juice added to the vinegar. You can combine them in a bowl and pour them down the toilet, and let the mixture sit for a couple of hours. It will probably take even less time to work, but if you are dealing with a severe stain, you can let it sit longer. Works best in a drained toilet bowl. 

Scrub before flushing if you need to. 

Combine Baking Soda and Vinegar

Another very powerful combination that works exceptionally well on limescale stains at the bottom of the toilet bowl is vinegar and baking soda. 

Start by draining all the water from your toilet bowl. Let it dry, and then sprinkle the bottom with roughly a cup of baking soda. Pour a cup of white vinegar over the baking soda. It will start to fizz and foam immediately, which is what you want. 

Wait until the fizzing stops and scrub away any leftover limescale, which should be softened and easy to remove. Flush when done. 

Use a Commercial Toilet Limescale Remover 

If you prefer to use a commercial product to get rid of the limescale at the bottom of your toilet, you can easily find one in your local supermarket or on Amazon. 

The HG toilet cleaner is a very good choice, and can tackle most limescale buildup. The Harpic limescale remover works well too. 

Dishwasher Tablets

Dishwasher tablets can also help you tackle the brown stain in the toilet. All you need to do is pop one into the toilet and let it dissolve. Give the toilet a bit of a scrub with a toilet brush, and let it sit for as long as you can. 

When your patience runs out, scrub again, flush, and hopefully the stain will be gone.

Borax Paste 

While you can’t buy borax in the UK, if you’ve got some from abroad, you can use it to get rid of the toilet stain. 

Make a paste out of borax and water, aiming to keep it on the thicker side. You want to make sure it sticks. Evenly distribute the paste on the stain and let it sit for half an hour. 

Gently scrub the paste and the stain away and flush the toilet. Make sure you wear gloves when handling borax. 

Hydrogen Peroxide 

If you have some hydrogen peroxide in the house, you can use it to eliminate the stain in the toilet. Pour half a cup into the bowl, after having drained all the water from it. Let it sit for 30 minutes, then scrub if you need to and flush. 


If you prefer scrubbing to letting a chemical do its thing, or if the stains at the bottom of your toilet are particularly difficult to remove, you can use sandpaper to scrub them away. 

Find a fine sandpaper that won’t damage your toilet, and don’t scrub too hard. Ideally, you will have used a cleaning agent first to loosen the stain up. Make sure you are wearing gloves. 

What Causes Brown Stains in Toilet Bowls?

The most likely cause of the brown stain at the bottom of your toilet bowl is limescale, which is in turn caused by hard water. The minerals in the water, most notably calcium and magnesium, will stick to the toilet bowl over time and cause discoloration and flaky buildup.

The stain will start out as white and powdery, and will over time become grey, green and ultimately brown. 

The brown stain can rarely also be caused by a buildup of bacteria. 

Wrapping It Up 

If you’ve started to notice a brown stain at the bottom of your toilet bowl, don’t freak out. It’s just a bit of limescale which you can get rid of with baking soda, vinegar, citric acid or a commercial limescale remover. 


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