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How to Remove Brown Stain in Bottom of Toilet Bowl?

Note: This post may contain affiliate links. This means that at no cost to you, we may receive a small commission for made purchases.

Many of us spend a lot of time each week cleaning our bathrooms to keep them sparkling and inviting.

That’s why it can be so frustrating when stubborn and gross-looking brown stains start to form inside our toilet bowls. 

If you’ve noticed a brown stain growing in the bottom of your toilet bowl, you’re probably eager to get rid of it as soon as possible.

However, there are a lot of myths on the internet regarding the best methods for cleaning these ominous stains.

Some of this misinformation could actually lead you to do more damage than good to your toilet bowl, so it’s important to know what you’re doing going into the process. 

Keep reading to find out the cause behind that annoying brown stain in your toilet bowl, why it’s important to remove it, and the best (and worst) methods of restoring your toilet bowl to its original state. 

What Causes Brown Stains in Toilet Bowls?

The chances are, when you first saw the brown stain in the bottom of your toilet bowl, you made an assumption about what caused it.

Considering the fact that our toilet bowls come into contact with some not-so-nice substances on a regular basis, you might think that the cause of the stain is obvious. 

However, you might be surprised to learn that the main cause of the brown discoloration in your toilet bowl is actually hard water. 

Hard water contains several important minerals that are beneficial to humans, including calcium and magnesium.

While you may have heard that hard water is damaging to human health, this is actually a myth.

Apart from causing dry hair and skin, there aren’t many negative effects of hard water on the human body. However, when it comes to our plumbing and toilet bowls, it’s a different story. 

For one thing, hard water is known to cause limescale buildups inside pipes and toilets. This limescale is the result of excess calcium and it can cause discoloration over time.

At first, limescale appears as a white, powdery substance. Over time, though, the limescale will start to go gray before turning green. If it’s not cleaned at this stage, the stain eventually turns brown.

This happens because of manganese and iron compounds acting on the limescale. 

The problem with brown limescale buildup is that it’s very difficult to clean. The longer limescale is allowed to build, the tougher it is to remove.

Luckily for you, we’re going to be outlining the best methods for brown limescale removal later in this article so you can get your toilet shiny and clean again. 

Why Should You Remove Brown Toilet Bowl Stains?

Removing a brown stain from the bottom of your toilet bowl definitely isn’t the most appealing household chore. You might be tempted to put it off for as long as possible because, let’s face it, it’s a pretty gross job. 

However, it is important to remove brown toilet bowl stains as early as soon as possible after you notice them – and not just because they don’t look good. 

If you leave limescale to build up inside your toilet bowl, you’ll be flushing mineral deposits down the toilet every time you use the flush.

This sends those deposits straight into your plumbing, where they will sit and accumulate. Eventually, the limescale might build up enough to restrict the flow of water in your pipes, which could cause a very serious plumbing issue.

So, if you don’t want to have to call in a plumbing specialist to fix your pipes at a later date, you should deal with the brown stain in your toilet bowl right now. 

Brown Stain Removal Methods for Toilet Bowls 

When it comes to cleaning the brown stain in the bottom of your toilet bowl, you will want to choose a cleaning method that is efficient and effective.

After all, you probably want to spend the least amount of time possible on this task, but you also need to make sure it’s done properly so that you can preserve the functionality of your plumbing. 

Here are the best ways to remove brown stains from the inside of your toilet bowl: 

Stain Removal Solutions 

The easiest way to remove brown stains in your toilet bowl if you don’t want to have to prepare your own cleaning solution is to buy a pre-made stain removal solution

Because these stain removers have been formulated by experts and are backed by science, you can be sure that they will be highly effective at getting rid of tough stains caused by limescale buildup. 

If you have a very stubborn stain in your toilet bowl, especially if it has been left to sit for a long time, a pre-made stain remover would be our top recommendation.

Whereas other methods of stain removal can be hit-and-miss when it comes to long-term toilet staining, a professionally-formulated stain remover is much more likely to be effective the first time. 

Baking Soda and Coca-Cola 

The combination of baking soda and coca-cola is well known for its cleaning properties. For this reason, many people find that it works wonders for removing limescale stains inside toilet bowls. 

If you’re wondering why coca-cola and baking soda works so well for removing these stains, it’s because it produces a chemical reaction with a high level of acidity, similar to vinegar.

Highly acidic substances dissolve limescale effectively, so you can see why this mixture is a good choice for this particular cleaning task. 

If you don’t have any coca-cola, you can even use baking soda by itself. However, for reasons that we’ll explain later, you shouldn’t try to use cola on its own to clean the limescale stain in your toilet bowl.


The reason why a coca-cola and baking soda mixture is such a great choice for cleaning brown stains in toilet bowls is that it has an acidity level similar to that of vinegar.

Therefore, it should come as no surprise that vinegar itself is an excellent cleaning agent for such stains. 

However, if you’re going to use vinegar to clean the inside of your toilet bowl, you can’t just pour a random quantity into your toilet and hope for the best.

If you want to really see results, you’ll have to pay attention to the quantities that you are using and how long you leave the vinegar to take effect. 

For the most effective clean, you should use a whole liter of undiluted vinegar. Pour the vinegar around the edges of the toilet bowl and then leave it to sit for 3 hours.

This is important because you need to give the vinegar time to take effect. Then, after 3 hours have passed, take a scrubbing tool like a sponge covered in white vinegar and manually scrub any remaining limescale away.

Thanks to the vinegar, it should come off fairly easily. Flush the toilet and then, if necessary, repeat the process. 

Lemon and Vinegar 

Lemon and vinegar are two acidic natural cleaning agents, so it makes sense that combining them would result in a very clean toilet

You only need to mix a few drops of lemon juice into the vinegar to see results. While using vinegar on its own will take about 3 hours, if you use lemon juice and vinegar together, you should be able to remove the limescale in as little as 10 minutes. 

Depending on the severity of the stain, you may not even need to scrub any limescale off the toilet bowl at the end of the process. In most cases, simply flushing the toilet after 10 minutes should remove the stain. 

Baking Soda and Vinegar 

Since you can use both baking soda and vinegar individually to clean brown limescale stains from the bottom of your toilet bowl, you can also double up and use them together for maximum cleaning power. 

This method of cleaning limescale stains in your toilet is a bit more complicated than some of the other solutions we’ve recommended, however. If you’re going to use vinegar in conjunction with baking soda, you should follow this step-by-step process: 

  1. Scrub the inside of your toilet with a toilet brush and some regular toilet cleaner. Make sure to scrub as far back into the u-bend as possible. 
  2. Leave the toilet alone for 30 minutes.
  3. After 30 minutes, flush the toilet
  4. Pour roughly 250 ml of cleaning vinegar into the toilet, aiming around the sides of the bowl. 
  5. Add 200 grams of baking soda to the toilet bowl. 
  6. Now pour in another 250 ml of vinegar. At this point, the mixture should be bubbling and fizzing. Don’t worry, this is normal and exactly what you want because it shows that the chemical reaction is taking place. 
  7. Leave the mixture to settle for approximately 5 minutes. 
  8. Use your toilet brush to scrub away any residual limescale. You shouldn’t have to press too hard with the brush because the baking soda and vinegar should have softened the stain. 
  9. Finally, flush the toilet. 


Ideally, you probably won’t want to rely solely on physical scrubbing to get the limescale stain off your toilet bowl. Let’s face it, nobody really wants to stick their hands into a toilet to clean it.

However, as a last resort to get rid of stubborn, brown limescale, you can use sandpaper. 

Go to your local hardware or craft store and buy both fine-grain and medium-grain sandpaper.

You’ll be using the medium-grain for most of the process. The fine-grain sandpaper is just for the finishing touches. 

First of all, put on your gloves, and get to work scrubbing the stain with the medium-grain sandpaper.

Try not to press too hard. Start softly and only scrub harder if the stain isn’t lifting.

Scrubbing excessively hard will just damage your toilet bowl. After buffing the stain with fine-grain sandpaper, you can finish the job by cleaning your toilet as usual with a toilet brush and toilet cleaner. 

How NOT to Remove Brown Stains in Your Toilet Bowl 

We mentioned earlier that you’ll find some misinformation online about the best ways to get rid of brown stains in your toilet bowl.

How to Remove Brown Stain in Bottom of Toilet Bowl?

Some of these methods are simply ineffective, while others could actually be damaging to your toilet and your plumbing. 

Even if you see them recommended by other sources, please don’t try any of the following methods for cleaning brown stains in your toilet bowl: 

Cistern Blocks 

You may have heard that cistern blocks are the best way to remove tough stains, including limescale buildup from the inside of your toilet bowl. 

A cistern block is a solid block of chemical substances that sticks inside your toilet bowl and dissolves, releasing chemicals that consistently clean the inside of your toilet. 

However, cistern blocks are only effective as a preventative solution.

That is to say, while using a cistern block might help to stop limescale buildups in the first place, they won’t be effective when it comes to removing stains that have already built up. 

Additionally, many of the cistern blocks available on the market are fairly toxic, so there are much better methods of cleaning your toilet without exposing yourself to these harsh chemicals. 


As we mentioned earlier, Coca-Cola on its own is not an effective toilet cleaning solution, especially when it comes to stubborn brown stains caused by limescale. 

You might be surprised to hear this because many of us have seen videos of dirty coins being cleaned in a glass of cola.

However, using Coca-Cola by itself to clean your limescale stain might backfire and contribute even more of a brown color to the stain, particularly if you follow some of the online advice that recommends leaving an entire bottle of cola to sit in your toilet overnight. 

Please don’t try to clean brown stains in your toilet bowl using only Coca-Cola. If you want to try using Coca-Cola to clean your toilet (after all, it’s easy and inexpensive), only do so in conjunction with baking soda. 


Bleach is known for being a powerful and highly effective cleaning agent, so many people are surprised when they hear that it’s actually not a good idea to clean brown stains in your toilet using bleach.

Unfortunately, the most bleach will do for your brown toilet bowl stains is make them seem lighter in color.

This is definitely not a good thing because it may trick you into thinking your toilet bowl is cleaner when, in fact, the limescale build-up is still there – it’s just less visible. 

Bleach can also oxidize your toilet water, and the combination of oxidized water and limescale is not a good one.

If anything, it might actually make the limescale more stubborn, meaning that other cleaning methods will be less effective

Final Thoughts 

Hopefully, you now know exactly what to do (and what NOT to do!) about that stubborn brown stain on the bottom of your toilet bowl (see also ‘Toilet Bowl Smells Like Urine‘). 

Remember, these brown stains are caused by limescale, which is notoriously difficult to remove and very damaging for plumbing.

Therefore, you should use one of the highly effective cleaning methods outlined in this article to resolve the problem at the earliest opportunity. 

Steer clear of Coca-Cola, bleach, and cistern blocks for this purpose. Instead, use pre-formulated limescale removers or natural cleaning agents such as vinegar, baking soda, or lemon juice. 

author avatar
Anthony Barnes
Anthony Barnes is the founder of Water Heater Hub and a second-generation plumber by profession. Before developing Water Heater Hub, Anthony Barnes was a full-time plumber, and he has undertaken a wide variety of projects over the decades. As a second-generation plumber, it was easy for Anthony to get used to the technicalities of all from a tender age


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