Black Sediment In The Toilet Bowl: 5 Reasons & Fixes


It can be most unpleasant if we have to use the bathroom at a wayside stop in a small town, and find dark stuff in the bottom of the toilet. We cover our nose, and flush and flush but the gunky stuff is still there. This means it’s not what you think, which may not necessarily be a bad idea.

Water travels a long way to reach your toilet tank. The best way to solve this problem if you have it is to test at each point. This includes checking neighborhood water quality, taking samples around the house, inspecting the flush mechanism, and looking inside the tank for mold. 

The best way to achieve this is to remember:

  • Find out whether this is a neighborhood problem.
  • Take water samples elsewhere in the house.
  • Locate and fix any leaking pipes in the garden.
  • Inspect the flush mechanism for wear and tear.
  • If you still have the problem, clean the toilet tank.

The Water’s Trip to Your Toilet Flush Tank

The water in your toilet flush tank traveled a long way to get there. It first fell to the ground as precipitation during rain, sleet, or snow. And after that it collected in a reservoir, flowed in a river, or filtered down into the earth.

It may have even gone up and down like a yo-yo in a hydro dam, but eventually it ended up in your utility’s supply dam. In the process of that journey it would have accumulated some dark sediment, which is your utility’s job to eliminate.

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The water would have left the utility sparkling clean and crystal clear. Then it traveled down pipes to your suburb, and finally ended up in your toilet tank. However, black sediment may have entered the system at some point, or germinated in the water after it arrived.

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Tracking Down Sediment By Process Of Elimination

We’ll follow a kind of split-half method to get to the bottom of the mystery. We’ll begin at the start of the journey, and take it from there.

1. The Sediment Comes From The Utility’s Side

It is quite possible the utility has a leak, or a pipe break somewhere on the supply line. This could draw particles from the earth into the water and cause the problem.

Ask your near neighbors if they have a similar problem. If they do, phone the utility and report the black sediment in your toilet bowl.

2. The Sediment Comes From Inside Your Yard

If your neighbors’ utility water is clear, then your problem is happening inside your yard. You may have a pipe leak, or a break in the garden drawing particles of earth through.

Take samples of water from your garden tap, your kitchen, your bathroom and anywhere else. Let these samples stand in clear glass tumblers for a couple of hours, then compare them.

If the water is murky, or there is sediment in the bottom of the tumblers, then you have a damaged pipe in your yard. Find a leak detection specialist. You may be able to fix the actual leak yourself.

3. The Pipes Are Intact But They Are Getting Old

Water supply pipes in old houses may be made of steel or iron. They will have been galvanized originally, but this sacrificial layer gets thinner and thinner until it fails. The rust you see on the outside actually begins on the inside. A rusty water pipe is ready to fail.

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Meanwhile the inner rust layer can discolor the water and even start flaking off. You have only three choices:

  • Put up with the dirty water but purchase clean drinking water.
  • Fit a water filter and have water samples checked regularly.
  • Install a whole new plumbing system – but this may not be necessary!

4. Your Toilet Tank Mechanism Is Getting Old

Your toilet flush mechanism has several waterproof gaskets to control water flow. Nowadays these are neoprene, but in olden days they were black rubber. That rubber eventually decays and accumulates on the bottom of the toilet tank.

It’s possible you may be able to get spares. If not, this could be a smart opportunity to replace the toilet tank

You may have heard stories about the black polystyrene float that also eventually fails. This is correct. However, the residue floats so it could never become sediment in your toilet bowl.

5. You Have Black Mold In The Toilet Tank

You may have noticed black mold in your bathroom, especially in spots where water lies for a while. Common places for this to appear include the shower floor especially if tiled, and the ledge around the rim of the bath against the wall.

Remove the toilet tank lid carefully, and set it aside on a soft surface. If you find the white porcelain inside the tank is coated with mold, then you may have finally discovered why you have black sediment in your bowl.

Now You Know The Problem, Let’s Fix It

If The Sediment Arrived Down The Water Supply

If the underlying problem lies with the supply pipes, we suggest you fix that first before you remove the black sediment, although you might still like to have an interim cleanup.

  1. Wear a pair of plastic gloves, with long cuffs that reach up to your elbows.
  2. Remove the toilet tank cover. Set it aside on a soft surface to discourage chipping.
  3. Study the layout of the flush mechanism. Operate it and observe the cycle.
  4. Locate a place where you can reach the tank bottom without touching the mechanism.
  5. Do a full flush of the toilet while you swirl your hand to agitate the sediment.
  6. Repeat the process several times until there is no sediment in the tank or the bowl.
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If You Have Black Mold In The Toilet Tank

  1. Pour two cups of neat vinegar into the tank. Wait twenty minutes.
  2. Wear a pair of plastic gloves, with long cuffs that reach up to your elbows.
  3. Scrub away at the black mold with a nylon scourer and washing-up brush.
  4. After a while, flush the toilet, review progress and continue scrubbing.
  5. When you are satisfied, clear the sediment as we described above.
  6. Clean the toilet bowl as you normally would, and you can use it again.

You may be able to control bathroom mold better, if you have the windows open when you shower, and install an exhaust fan. However, you may still have to clean the toilet tank from time to time, repeating the above steps.

Your Takeaway To Remember

Sediment in your toilet tank may enter the pipes at any point in the system. Check utility water quality first, and then take samples in your home. After that inspect the toilet mechanism and look for mold in the toilet tank. Fix the problem wherever you find it, and you should eliminate black sediment in your toilet bowl.