There’s almost nothing worse than a dirty toilet. But what’s happening when your toilet is clean, and the water in it is brown?

The most likely reason that your toilet water is brown is that there is rust somewhere in your system. Older galvanized pipes can rust, and the rust will cause discoloration in your water. Your water supply could also be rich in iron compounds.

While the rust itself isn’t a health hazard, it can potentially stain the toilet and promote the growth of nasty bacteria. In this article, we will provide a guide to finding out why there is brown water in your toilet. These reasons include rusted galvanized pipes, hard water mineral build up, a clogged pipe, or a damaged well system.

1. Day to Day Use

Your first step to troubleshooting the brown water in your toilet should be to flush the toilet. There’s a chance that your toilet didn’t completely flush its contents, and perhaps needs another chance to clear out.

If more brown water rushes into the bowl, you have a more serious problem on your hands.

2. Rusted Pipes

Next, check the colour of the water in the rest of your house. Check the taps and shower in the bathroom, and check the water in the kitchen sink and any other bathrooms you may have.

If the water in the entire house is brown, the problem is not restricted to just your toilet. You have a plumbing issue affecting your entire house. The most likely cause of this is a surplus of iron in your water.

It is likely that the pipes bringing your water supply are corroded. Pipes installed before 1960 were often made of iron. These old pipes could be rusting, and the segments of rust are bleeding into your water supply and discoloring it.

Other signs of this could be water that tastes like metal, and rust-colored stains on your clothes after you run them through the washing machine

If this is the case, then you most likely have a costly journey ahead of you. A professional will need to be brought in to assess the situation. They may suggest replacing all of your pipes, which is expensive, but necessary for a long-term solution. If you’re lucky, it may just be a single pipe leading into your home that needs replacing.

In the short term, you may be able to solve your problem with water additives.

Water Softeners

Water softeners and other chemical additives can lower the iron content in your water. They also help to get rid of iron bacteria in your water. This solution will not remove all traces of iron from your system, but, especially if paired with an iron filter, it can be a short-term solution to your rusty pipes.


Chlorine has been proved to be an effective agent when used against iron bacteria. It forces the iron particles to oxidize and the bacteria to be removed. It again won’t fix your rusted pipe issue altogether, but it can be used in the short term to kill iron bacteria in your water.

3. A Damaged Well

If you have a well, the brown color in your toilet could also be caused by dissolved organic matter in your well. The disclosed water may also contain sediment. Usually this means that your well has been compromised somehow. It may have been damaged by a storm, or some recent landscaping or construction.

When wells are damaged, it is professionals who should take care of the repairs to the system.

4. Rusted Toilet Parts

If you’ve checked all of the water in your house, and it’s just the water in your toilet that is brown, then you have a localized issue.

You could still be encountering a rusty pipe. It could be that your toilet is hooked up to a different water line than the other faucets in your house, and that pipe is rusted. It could also be the inner components of the toilet itself that are rusted.

Check the back tank of the toilet to see if there are any obvious parts that have been rusted or damaged. If you can’t see anything, you can safely assume that it’s either the toilet’s connection to the water or the pipe that delivers water to your bathroom that is rusted.

5. Hard Water Mineral Build Up

If you have a new plumbing system and you feel as though rusted pipes couldn’t possibly be your problem, there is another reason your toilet water may be brown. Discolored toilet water is a possible signifier of clogged sewer pipes.

Your pipes could be clogged by hard water minerals. When manganese and calcium come into contact with the oxygen in your toilet tank, they turn the water brown. These minerals can enter your system through the use of certain toilet cleaners.

When certain cleaners are flushed through your toilet and enter your sewer line, they can build up over time. These build-ups can become blockages. The blockages then restrict water movement throughout your plumbing, and the water is backed up into the toilet bowl where you can see the brown discoloration of the water.

The minerals may attack your system by rusting the metal components of your tank, forming a thick layer of build up on your tank, and creating a sticky surface that could potentially catch and hold other debris, hardening and creating more permanent blockages. Pieces of these could also break off and the hardened chemical debris could float throughout your system.

To fix these chemical blockages, you may be able to clean the water tank yourself. It can be tricky depending on how long the minerals have been building up in your system. Some at-home remedies include soaking the components of your toilet tank with white vinegar. This can possibly break apart the mineral build up.

6. A Clogged Pipe

Somewhere in your plumbing system, you could have a blocked pipe. This can result in particles backing up into the toilet bowl. To remove the blockage, it’s likely you will need to call a professional. They will have the tools and skill to properly clean your line.

It is important to fix this blocked sewer line as soon as possible. Blocked pipes can crack or burst open from the built up pressure. If this happens, the cost of repair will be much higher than just clearing the blockages now.

You will also have a mess to clean up somewhere in your plumbing system. The burst pipes can contaminate your house with water, that can lead to the growth of mold, wood rot, and other issues.

Calling a Professional

Unfortunately, most plumbing issues need to be tended to by a professional. These include the ones that can cause brown water in your toilet bowl. When you do call a plumber, feel free to include the information that you’ve collected yourself about your plumbing system. Also, tell them what year your house was built, and the last time that your plumbing was properly serviced.

Is Iron in Your Water Dangerous?

While having a high iron content may be unappealing, the iron itself is not dangerous. The iron may cause other problems that are dangerous, however.

When iron is in your plumbing, it can cause discoloration to your toilet bowl. This discoloration can then stain your toilet bowl, and can promote the growth of harmful bacteria.


The most common cause for brown water in your toilet is rust. This rust can be affecting your entire plumbing system, or just the pipes leading to your toilet.

The discoloration could also be caused by a well issue, or a blockage somewhere in your plumbing.

If in doubt, call a professional before taking on the project yourself.

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