What Causes Black Stains in Toilet Bowls? (How to Clean & Avoid Them)

If you’ve ever lifted the toilet lid and been greeted by disgusting black stains in the toilet bowl, you know how gross and uninviting they can be. They probably don’t smell too great either! 

While black stains in a toilet bowl can be caused by many things, mineral deposits from hard water are the most common culprits. To get rid of them you will have to do some tough scrubbing and then you should prevent them from coming back by removing the harsh minerals in your water with a water softener. 

Keep reading to find out more about those pesky stains in your toilets. I’ll explain everything you need to know about cleaning them up and keeping them from coming back.

Common Causes of Black Stains in the Toilet

As I mentioned, those black stains in your toilet bowl are usually caused by mineral deposits left behind from hard water but mold can also be a factor.

Both of those usually occur in areas where there is little movement of water. For example, a toilet that sits unused for long periods of time. 

High levels of manganese

Manganese is one of the most common metals found in our environment, and it occurs naturally in soil, air, food, and water. However, high levels of manganese in the water can lead to stains on your porcelain fixtures that are hard to get off. It’s often accompanied by a foul odor as well. 

And with high levels of Manganese in your water, toilet bowl stains might be the least of your worries since they can cause build-up in the pipes over time which can cause problems with the flow of your plumbing system.

If you suspect that your water contains excessive amounts of manganese, I recommend contacting a water treatment professional to perform a water analysis. They’ll use sophisticated equipment to measure the concentration of manganese in your water and determine whether there is a problem.

High levels of calcium

Calcium is found in soil. As rain falls, it dissolves some of the soil particles and carries them down into rivers and streams. Some of these dissolved particles end up in your water which then goes through your pipes and finds its way into your toilet causing black stains.

To prevent black staining, I would try using any kind of acidic cleaner. Vinegar would work as well. The acid will dissolve the mineral deposits making them easier to brush away.

Some people also recommend adding baking soda to your toilet tank. Baking soda neutralizes the acidity in the toilet and prevents calcium from forming. Just add two teaspoons of baking soda to each gallon of water used for flushing.

High levels iron

If there are high levels of iron in your water, there is also a higher chance that there is rust in your pipes.

This problem is especially prevalent in older homes since older plumbing systems used lead solder to join copper pipes together. Lead solder contains small amounts of iron. When the water runs through the pipes, the iron combines with the oxygen in the water to form rust.

Flushing your toilet regularly will help remove some of the iron from the pipes and help avoid stains, but for a long-term solution, adding a descaler to break down the iron deposits in the pipes will work. They contain chemicals that react with the iron to create a chemical reaction that breaks down the iron.

Mold is growing in your toilet

Unlike black stains that come from minerals in hard water, black stains that come from mold are usually a bit easier to deal with. But that doesn’t mean they are any better. In fact, they may be more dangerous. 

Since mold grows best in warm, humid conditions, it thrives in places like bathrooms and yes, your toilet bowl. There is usually stagnant water sitting inside your toilet tank, so when you flush your toilet, the mold spores can spread into your toilet bowl and throughout your entire bathroom.

If you have any black mold sitting in your plumbing pipes because of condensation, those spores can also make their way into the toilet bowl. 

Make sure to get rid of any mold with a bleach-water solution as soon as you spot it to prevent it from spreading anymore. You can pour a cup of bleach into the tank and flush it to remove any remaining mold throughout the system.

How to Test the Minerals in Your Water

Water testing kits are available at most hardware stores. They come in two varieties: colorimetric and turbidimeter. Colorimeters measure the amount of iron present in the water. Turbidimeters measure the amount of suspended solids in the water. Both tests work well, but colorimeters tend to be less expensive.

A water treatment professional can also help you determine if there is a high mineral content in your water. They will test your water for hardness, alkalinity, pH levels, iron, calcium, magnesium, total dissolved solids, and more.

An expert can provide advice on which types of equipment to buy to treat your water if they do find anything off. 

How to Fix the Black Stains in Your Toilet Bowl

There are so many ways to clean your toilet bowl and everyone seems to have a preferred method. Depending on the cause of the stain, one cleaning method may work better than others. 

Some use borax to treat the problem, while others prefer bleach or vinegar. I’ve also heard of using hydrogen peroxide. And I know this sounds unusual, but Coca-Cola can also be used to clean black water stains that are caused by iron and manganese.

Let’s take a look at a couple of things you can do to get rid of the stains and prevent them from coming back anytime soon. 

Deep clean your toilet

First, get rid of the stains that already exist by giving your toilet a deep clean. First, make sure to put your gloves on before starting your cleaning process so that you can really get a deep clean. In addition, make sure you are not putting harsh chemicals and cleaners in your toilet as it can damage your pipes and system.

Start by cleaning the outside of the toilet with a disinfectant spray to get rid of all the bacteria around it. Once you’ve cleaned the outside, you can proceed with scrubbing your toilet bowl. There are many things you can use to clean your toilet bowl.

Baking soda and ammonia are both popular toilet cleaning products because they help break down the gunk inside your toilet. Vinegar is also an effective cleaner and it also makes everything smell good. You can also use hydrogen peroxide to clean a black stain. And as I mentioned before Coca-Cola can also be used to clean black water stains that are caused by iron and manganese.

Finally, don’t forget the tank! A dirty toilet tank leads to a dirty bowl. To clean it, turn off the water supply and let the tank drain completely. Then fill the tank with vinegar up to the overflow valve. Let it sit in the tank overnight before flushing it down the toilet. Scrub any remaining grime out with a scrub brush and a cleaning solution that doesn’t contain bleach, since bleach is corrosive and can damage the tank. 

Flush your toilet more frequently

Now that you’ve cleaned your toilet, you should try to keep the stains from coming back. One way to do that is to flush your toilet more frequently.

If you don’t flush your toilet regularly, the water remains stagnant which can be a perfect breeding ground for mold and bacteria to build up inside the bowl. That’s when we really start to see the black stains around the bowl. 

For toilets that are used regularly, this may not be the issue, but you should also go around your house flush toilets that you don’t get used very often so they don’t get stains. 

Install a water softener

If you have tested your water and found that you have hard water, I recommend installing a water softener on your main water supply. Water softeners work well at removing calcium and magnesium from tap water, two other elements that contribute to black staining.

It will not only prevent those pesky stains from forming in your toilet bowls, but also be better for your plumbing pipes, water heater, and washing machine since mineral buildup can wreak havoc on these systems.

A water softener sends water through a tank filled with resin beads that look a bit like coffee grounds. These beads act as a magnet for all the harmful metals and minerals in your water and absorb them from the water before sending it back out of the tank and into your house. 

When those resin beads fill up with too many minerals, the water softener will flush them with a salt solution held in a second tank. The hard minerals then go out to drain, and the resin beads are ready to soften your water again. 

When Should You Call a Professional?

Cleaning your toilet can certainly be done without the help of a professional. You should clean your toilet and all its parts regularly if you want to prevent stains. 

Using agents that keep your toilet fresh and help minimize the mineral buildup like a descaler can also be used without the supervision of a plumber.

But when it comes to a more long-term solution, like testing your water quality and installing a water softener if needed, I would recommend hiring a professional. They will be able to recommend the perfect water treatment system customized for your water situation and help you install it. 


So while hard water can leave you with an unpleasant situation when you lift up the toilet lid, there are many DIY solutions to get rid of them. 

I hope that with my advice you are able to keep the stains at bay and maybe even decide on a permanent solution with a water softener. Your toilet – and everything else with water running through it – will thank you.

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