
If you’re like me, you likely try to spend as little time looking down the toilet bowl as possible. And the only time you open up the toilet tank is if there’s a problem.
Noticing black sediment in a toilet bowl or tank is a problem you’ll need to spend a little time rooting around in there to fix.
And we’ll show you exactly what to look for and how to fix it below…
So what causes black sediment in a toilet bowl, and what’s the best way to remove it?
Black sediment in a toilet bowl or tank is usually caused by the breakdown of your toilet fittings. Mold, excess minerals, or water supply contamination are less common causes. Several solutions include replacing your toilet tank, installing a water softener, or contacting your water supplier.
This table will help you to diagnose and fix black sediment in your toilet bowl or tank.
Cause | How to identify | Fix |
---|---|---|
Breakdown of toilet float or waterproof gaskets in toilet tank | – Small pieces of black rubber, neoprene – Plastic residue in tank or bowl | – Replace the worn-out parts with spares – Alternatively, replace the tank |
Mineral deposits | – Black stains and deposits in toilet and other fixtures | – Clean the tank and bowl thoroughly – consider installing a water softener to remove minerals |
Mold | – Black rings in toilet bowl – Mold-like black growth on surfaces ofthe toilet | – Clean toilet thoroughly and regularly |
Rusty pipes | – Rusty pipes on lead up to toilet – Discolored water flowing into the tank | – Replace rusty pipes |
Problems with the water supply (city water) | – Sand or silt-like particles in the tank or bowl – Neighbors also report the same problem | – Contact the local water supplier |
Problems with the water supply (private well) | – Sand or silt-like particles in the tank or bowl – Faucets also have the same problem | – Check your filtration system is working correctly – Consider upgrading to a lower-micron sediment filter |
Let’s find out how to identify and fix each of these problems in more detail.
Common Causes of Black Sediment in Toilet Bowl or Tank & How to Fix
Most causes of black sediment appearing in your toilet are easy to diagnose and fix yourself. However, if the problem is with your water supply, you may need to contact your water supplier or call a professional to look at your filtration system.
Breakdown of toilet float, flapper, or gaskets in the tank
Toilet floats, flappers, and gaskets are all prone to breaking down or disintegrating over time. This can be made worse by using cleaning products like bleach tabs that are put into the tank [1].

What to look for: If your toilet has a disintegrating float, you’ll notice black rubber-like pieces in the tank [2]. These shouldn’t find their way into the toilet bowl, because, by definition, the material is made to float.
If a flapper or gasket has broken down, you may notice plastic- or rubber-like pieces in the toilet bowl and the tank.
Solution: Search online or head to your local hardware store and look for spare parts. If the spares are difficult to find, you may be better off replacing the tank entirely.
Excess mineral deposits in your water
Hard water is water with high levels of minerals. In areas where hard water is present, you may notice build-ups of scale.
Usually, deposits caused by hard water are white; however, high levels of manganese can cause black scale and stains to build up [3].
What to look for: Black or dark brown deposits or rings on and around your toilet. These deposits may also be accompanied by discolored water.
Solution: Have your water tested to determine the levels of minerals, iron, or manganese present. For higher levels of manganese or iron, consider installing a water filter for well water. A water softener will be a better option for hard water with low levels of iron or manganese.
See our articles The Best Iron Filter for Well Water or The Best Water Softener for Well Water, depending on your situation.
Mold
When people say they see black sediment in their toilet, they’re often mistaken. Mold is commonly to blame.

If a toilet hasn’t been used for a long time and it’s also not been cleaned, it could create an environment favorable for mold growth [4]. It’s not a great situation to deal with, but there’s no need to worry as it’s not as serious as mold in drinking water.
What to look for: Black mold is pretty easy to spot. Look for black, almost fluffy-looking growths that look like they are spreading across your toilet surfaces or inside the bowl or tank.
Solution: Make sure you address the problem head-on. Mold grows best in warm, damp, and dark places. So open a window, let some light in, and ensure surfaces are wiped dry after use.
Next, clean the toilet thoroughly to get rid of the mold. There’s more on exactly how to do this below.
Rusty pipes
Rust starts inside old pipes, and at first, you’re unlikely to notice or detect it. Eventually, the problem gets so bad that pieces of the pipes start flaking off, and you may see this in your toilet system or your drinking water.

What to look for: If you notice black or red particles that look like mold in your toilet, check to see if they are coming from other faucets and bathrooms in the house. If not, a section of piping connected to the toilet has likely rusted.
Then give pipes a visual inspection from the outside. If you can see any pipes visibly rusted on the outside, you’ve probably found the source of the problem, and these will need replacing immediately.
Solution: First, flush the toilet continuously for 5 – 10 minutes to flush out any small pieces of rust that have broken off. If the problem persists, you’ll probably need to change the pipes.
Problems with the water supply (city water)
If you use city water, your local supplier will usually contact you if there are issues with the water. These warnings often come as a text message or an automated phone call.
What to look for: Check if the black sediment is only coming from your toilet or all your faucets and plumbing appliances. If the sediment is visible everywhere in the house, it may be a problem with your supply.
The second step is to get in touch with your neighbors. If the water supply is to blame, they will likely be experiencing the same problems.

Solution: Look for your local water supplier’s contact details and report the problem. It may be a good idea to switch to drinking bottled water until you receive notification that the problem has been fixed.
Problems with the water supply (well water)
Well water is a fantastic way to live ‘off the grid’ and save money on water bills. But you’re responsible for your water supply, and issues like black sediment appearing can occur.
What to look for: If sediment appears in your toilet and other places in the house, your well may be to blame. Take samples from around the house and let the water settle for a few hours.
Check your filtration system. The first stage is usually a sediment filter. Most modern sediment filters for well water have a clear window; if the filter mesh is visibly dirty, the system needs flushing. If you don’t have a sediment filter yet, I’ve reviewed several of them already. You can read our article about the best sediment filters for well water by clicking here.
After flushing the system, check the mesh for signs of wear and tear. If the filter mesh is broken, it’s not operating properly.
If the system is working correctly but needs flushing much more frequently than usual, check around your backyard and the area around your well for evidence of broken pipes or dirt and soil getting into your water supply.
Solution: Flush your sediment filter. If you regularly forget to do this, consider upgrading to an auto-flush model like the iSpring WSP50ARB Spin Down Sediment Filter, which you can program to flush at regular intervals.
Replace the broken filter mesh; these are available cheaply from the filter manufacturer. Consider going for a higher or lower micron rating. If the sediment in your water is large and you have other filtration stages, you may be able to get a larger micron rating (mesh with larger holes) which will get clogged less often.