Black Stains In Your Toilet Bowl? How To Remove Them

If you’ve ever walked into the bathroom and noticed black stains in your toilet bowl, two thoughts probably cross your mind simultaneously: where did the stains come from, and how can you get rid of them fast? Unsightly stains could be dangerous mold, so it’s crucial to remove them quickly.

what causes black stains in your toilet bowl

In this article, we’ll discuss what causes the black stains in toilet bowls and how you can get rid of them so you’ll never have to deal with an unsightly toilet again.

What Causes Black Stains In A Toilet Bowl?

There are a few different things that can cause black stains in toilet bowls. Let’s take a look at a few of the most common issues you might face (for brown/rust marks, see our separate article, and for yellow stains see this guide).

Mold And Mildew

If you have a toilet that isn’t used frequently, like in a guest bedroom, you may find mold or mildew can grow inside, leaving a black stain.

Since they thrive in dark, damp environments, mold and mildew can also grow inside your toilet’s water tank if you don’t use a drop-in cleaner tablet.

Mineral Deposits 

If you have hard water, mineral deposits from the water can cause black stains in your toilet bowl. Iron and manganese are the two most likely culprits, and they typically affect those with well water.

You can remove these deposits permanently by installing a water-softening system (you can also use WD-40 for this).


If you don’t clean your toilet bowl regularly, bacteria can grow inside the bowl and leave black stains. 

How To Get Rid of Black Stains And Spots In A Toilet Bowl

Since you have a good idea of what’s causing the marks in your toilet bowl, check out a few easy ways to remove them and keep them from coming back.

cleaning a toilet bowl

Clean Your Toilet

The first thing you should do when you notice black stains or spots in your toilet bowl is clean the toilet thoroughly. 

  1. Grab your toilet brush and toilet bowl cleaner.
  2. Turn off the water to the toilet and flush to remove as much water from the bowl as possible.
  3. Apply an ample amount of toilet bowl cleaner just under the rim of the toilet, letting it run down the sides to cover the entire surface of the bowl (never use this on the shower).
  4. Let the cleaner sit for 10 minutes so that it has time to permeate the stains.
  5. Dip your toilet brush into the water to wet it, then use it to thoroughly scrub the inside of the toilet bowl. Pay close attention to the underside of the rim since mold and mildew are likely to accumulate there.
  6. Turn the water back on and flush the toilet to rinse away loose dirt.

Repeat steps 1-6 as necessary to remove all black marks from your toilet bowl.

Use a toilet tank drop-in tablet to keep stains from coming back as frequently.

Remove Mineral Deposits 

If a thorough cleaning didn’t remove all the stains from the bowl, you probably have mineral deposits rather than or possibly in addition to mold.

Here’s how to get rid of them:

  1. Put vinegar in a spray bottle and spray it onto the rim of the toilet, making sure to fully saturate the stained area.
  2. Let the vinegar stand for 5 minutes to fully permeate the stains. Try to not let it dry all the way, and apply more vinegar if it does.
  3. Sprinkle baking soda onto the vinegar.
  4. When the vinegar and baking soda mixture stops fizzing, scrub the area with your toilet brush.
  5. Flush the toilet to remove loosened dirt.

Clean The Water Tank

If you’ve removed the mold and mineral deposits from your toilet bowl but you still see little black specks when you flush, the problem might be inside your toilet tank.

We don’t think about that area all that often, but since it’s a dark, damp area, mold and mildew can grow inside it. When you flush, pieces of that mold can break off and enter your toilet bowl.

Here’s the best way to clean your toilet’s water tank:

  1. Apply toilet cleaner to the inside of the holding tank.
  2. Let the cleaner sit for 10 minutes to permeate the stains.
  3. Scrub the tank using a fresh toilet brush. You should label your brushes, so you don’t introduce new bacteria into the water tank by using the same one that you use inside the bowl.
  4. Flush the toilet to remove loose dirt from the tank.

Get A Water Softener

If you discover that the black stains in your toilet bowl are caused by mineral deposits, you should consider installing a water softener to remove those minerals from your water.

Clean Your Toilet Regularly 

Now that you’ve removed all the black stains from your toilet, you need to make sure you clean your toilet regularly to keep them from coming back.

It can be easy to forget about toilets that aren’t used frequently, so coming up with a weekly cleaning schedule might help you keep on track.

Is Black Mold In The Toilet Dangerous?

All mold growing inside your home presents a health hazard. Prolonged exposure to mold can make you quite ill, so it’s best to remove it as soon as you can.

What Is The Black Stuff Floating In The Toilet After Flushing?

If you see black specks in your toilet bowl after you flush, it likely means that your toilet’s water tank is dirty.

Mold and mildew thrive in the dark, damp environment of a water tank, and those specks you see in your toilet bowl are little pieces of that mold falling apart and entering the water.


Looking into your pristine, white toilet bowl and noticing black stains can be unsettling. Not only do they look bad, but if they’re caused by mold or bacteria, they can also be hazardous to your health. 

Black stains in your toilet bowl can also be caused by mineral deposits like manganese or iron, particularly if you have a well. These deposits won’t harm you, but they still make your toilet look dirty.

If you see black specks floating in your toilet bowl after you flush, there’s probably mold or mildew growing in your toilet’s water tank. After you clean out the tank, you should use a drop-in cleaning tablet to keep them from coming back.

To keep your toilet looking its best, be sure to clean it regularly. If your stains are caused by mineral deposits, you can keep them at bay by installing a water softener.

Shauna Stone