How to Clean a Toilet Siphon Jet, Step-by-Step

Toilet siphon jets are the small openings underneath the inner bowl of your toilet’s rim and are typically an afterthought until they become clogged up with mineral deposits and bacteria. It is important to clean these jets before it becomes too much of a problem.  

diagram of siphonic jet

Bacteria forming on your toilet’s siphon jets can quickly become an issue of your health whenever you use the toilet. Mineral deposits, while not hazardous to your health, can clog up these siphon jets and can become hazardous to your toilet’s health.

In this post, we will go through a step-by-step guide on how to clean these toilet siphon jets and why it is an important thing to do on a regular basis. 

You’ll also see how to spot bacteria and mineral deposit growth on your siphon jets as well as some common mistakes to keep in mind when doing this job. Read on so you can get this simple, yet absolutely necessary task done with ease even if you have never done it before.

Why Should You Clean Your Toilet’s Siphon Jets?

Your toilet’s siphon jets are a necessary part to flushing the toilet and refilling it with water. If these jets become blocked or clogged up, your toilet may not refill all the way which can cause a whole array of other problems to take place that can get worse over time.

Also, bacteria can easily find its way into these jets and onto your body if they aren’t kept clean. You don’t need to be a germaphobe to realize that this can have a bad effect on your body after you use the toilet so many times.

How to Clean Your Toilet’s Siphon Jets

There are two ways to clean these jets, one for bacteria and one for mineral deposits. They are fairly similar but there’s a few key differences that are necessary to get one but not the other. Let’s begin with bacteria:

Cleaning Bacteria Off of Toilet Siphon Jets

Step 1: Pour a Bleach Solution Into the Toilet’s Overflow Tube

A toilet’s overflow tube is a pipe made of metal or plastic that runs up vertically in your toilet’s tank. Typically, there is another plastic tube clipped on top of it. 

Make sure the bleach solution is one part bleach and at least ten parts water. Bleach is a strong chemical that can damage your toilet and siphon jets if it is not diluted so, if you are not sure if the solution is exactly 1:10, play it safe and add more water.

Step 2: Let the Bleach Solution Sit, Then Flush

You should let the bleach solution sit for about 5 minutes before flushing it through your siphon jets. This solution should kill any bacteria that are around the siphon jets and clean out the toilet’s bowl for the step 3.

Step 3: Clean the Siphon Jet’s Holes and Repeat Step 1

Using a wire, scrape around all of the jet holes and use a hand mirror so you can see what you’re doing and that you have gotten every hole. 

You will want to wear a pair of rubber gloves for this step because you will have to get fairly hands on when it comes to cleaning out the jets. Once you are finished with scraping with the wire, use a scrubbing pad and chemical bowl cleaner to clean around all the jets as well. 

Lastly, make another bleach solution and repeat step 1 and there should be no bacteria around your siphon jets. Give them one last look with your mirror used earlier and see if there are mineral deposits around to also clean out. If you find some of these mineral deposits, follow the steps below.

Cleaning Mineral Deposits Off of Toilet Siphon Jets

Step 1: Pour Hot White Vinegar Into the Toilet’s Overflow Tube

If you don’t know where your toilet’s overflow tube is, refer to step 1 for cleaning bacteria above. Other than that, this step is essentially the same as the one for cleaning bacteria off of your siphon jets except with a different liquid.

Unlike bleach, vinegar will not harm your toilet, so you do not need to dilute it with water. Simply heat up roughly 8-12 ounces of vinegar to the point where you see steam coming off it and pour it into the overflow tube.

Step 2: Let the Vinegar Sit, Then Flush 

You will have to wait around 30 minutes so that the vinegar mixes with the toilet’s water to break down any mineral deposits properly once you flush. Be sure to mark the time when you should flush and once it’s done, you can move on to step 3.

Step 3: Scrape Out the Jets and Flush Again

Using a small allen wrench, start scraping any mineral deposits you see inside of your toilet’s siphon jets. As the mineral deposits begin to clear out, use a larger-sized allen wrench until the jets’ holes are completely cleared out.

Remember to flush every now and again to wash away any loose mineral deposits and double check your progress using a hand mirror. Again, you should use rubber gloves for this part to make sure your hands don’t get too dirty.

Once all the jets look clean and free of any bacteria or mineral deposits, give the toilet one last flush and call it a job well done.

How to Identify Bacteria and Mineral Deposit Buildup

If you have never done this task before, it is a good idea to take a look and see whether or not you’re already experiencing some bacteria or mineral deposit buildup on your siphon jets.

Black or dark orange spots around your toilet’s siphon jets will usually indicate there is some bacteria buildup. In this case, you should use the bleach solution and follow the steps above for cleaning off bacteria.

Anything that looks lightly colored and scaly around your siphon jets are probably mineral deposits. In this case, use the hot white vinegar and follow the steps above for cleaning mineral deposits.

You can also have both problems at once, in which case, you will see the visual indicators for both. If you see this, you will need to do both cleanup methods separately and leave around an hour or so in between doing both tasks.

Common Mistakes

Sometimes, the bacteria or mineral deposits will be really stuck on there but you should not try to scrape it off with excessive force. This could cause a crack or otherwise damage the porcelain around the toilet or the jets themselves which can lead to much more pricey repairs. 

Making sure the solutions are prepared properly is also very important. The bleach solution should be at least 10 parts water and the vinegar should be hot but no boiling. Both of these can damage your toilet’s overflow tube and siphon jets if prepared incorrectly.

Lastly, be sure to let these sit in the overflow tube for the specified amount of time. You have to let both the vinegar and bleach solution mix with the water for a while so it does not damage your toilet. Flushing too quickly can cause more harm than good even if your siphon jets are suffering from some pretty thick gunk. 


You, unfortunately, do not hear many people talk about cleaning their toilet’s siphon jets as a regular task for keeping up their toilet’s performance. This job is one of those that can save you all kinds of money by just checking on it every month or so.

Be sure to follow the steps for both cleaning bacteria and cleaning mineral deposits closely and remember how to find the warning signs of this buildup. 

Also keep in mind the common mistakes and you will be good to go and finish up this easy task that everyone should do to keep their toilet clean and happy.

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