Clean Toilet Smells so Bad? Why and What to Do

Toilet Smells Worse after Cleaning?

Sewer smells in the house can emanate from any drain but in most cases they can be traced to the toilet. So, why would a toilet still smell so bad despite being thoroughly cleaned?

A smelly toilet is caused by low water level in the bowl, clogged plumbing vent, dirty toilet tank, damaged wax ring or loose toilet bolts. Bacteria from the sewer may also find their way into the bowl and collect under the rim causing a horrible odor.

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Sometimes the smell is a very distinct urine smell and not just any sewer smell. In this case, the male members of your family are usually the culprit.

If your toilet smells of urine despite cleaning it, the male members of the family (especially young boys) have a poor aim of the bowl. This causes urine to collect under the toilet seat mounting, between tank and bowl, or under base of the toilet, which smells horrible after drying. Have them sit on the bowl when urinating.

To remove sewer/urine smells from a toilet, adjust the water level in the toilet, check if the plumbing vent is clogged, tighten loose toilet bolts or replace damaged wax rings. If the tank is the culprit, drain out the water and replace it with vinegar. Drain the vinegar after an hour and scrub gunk off the tank.

A sewage smell coming from a toilet is usually caused by a clogged drainpipe or vent stack, which force sewer gases out of the toilet bowl. Low water level in the toilet trap will also allow sewer gases through, and hence the sewage smell.

In rare cases, a hairline crack on the toilet bowl can cause waste to leak out and pool on the base of the toilet or leak in the flooring. Again, this will result in a sewage/urine smell in your house.

Smelly Toilet Remedy: How to Fix Clean Toilets that Smell so Bad

As I have already mentioned, a clean toilet that smells so bad can be caused by many things. You can therefore be stuck on where to start troubleshooting.

There is however a method you can use to troubleshoot the problem and fix it faster. Ask yourself this questions:

  • Is there a urine smell and not just any other smell?
  • Is the water level in the bowl too low?
  • Are other fixtures draining slowly and toilet having a poor flush?
  • Is there water pooling at the base of the toilet.
  • Is the toilet rocking?
  • How often do you clean your toilet tank

If you can answer the above questions, getting rid of the toilet smell will be easier and quicker.

1. Toilet Smells of Urine despite Cleaning

If there is a lingering urine smell from your toilet despite your best efforts to clean it, we can then be in agreement that your cleaning technique or frequency is not the problem, although your guests may not see it that way.

Whenever there are complains about a urine smell from a toilet, male members of the family are always at fault. You see, unlike females who pee while seated, males prefer to do the same while standing.

There is usually no guarantee that all the pee will safely land inside the bowl. The initial stream of pee is likely to shoot past the bowl and accumulate under the toilet seat mounting, or where the tank is joined to the bowl.

Both of these places are usually very hard to reach and clean. Fresh pee will not stink. However, after the pee dries up a very strong urine smell will reign supreme in your bathroom.

Another place that urine can accumulate and hide is the little space between the bottom of your toilet and the floor, especially if the toilet is not caulked.

It gets even worse if the floor is wooden, as the urine seeps inside the flooring and you will always have a urine smell no matter how well and frequently you clean the toilet.

The solution for this problem is an easy one. Just sit down with the male members of your family (especially young boys) and ask them to use the toilet while seated if they can’t get their aim correct. No diving!

2. Adjust Water Level in the Bowl

There is always a small amount of water at the bottom of the toilet bowl. This is made possible by the innovative U-bend called a P-trap.

The P-trap helps us to pick up things from the toilet when we drop them to avoid clogs in the drainpipe, and also helps in creating a siphon to flush the toilet.

Most importantly, the P-trap allows the bowl to always have some water. This water acts as a barrier, preventing sewer gases from coming up through the toilet, and instead do so from the plumbing vent.

For the trap to work as designed, the water level in the bowl needs to be just right. If it is too low, some sewer gases will manage to escape through and hence a smelly toilet despite it being clean.

The water level in the in the toilet bowl is directly proportional to the level inside the toilet tank. If the water level in the bowl is low, there is a chance that the water level in the tank is low as well.

To be sure of that, remove the toilet tank lid and check the water of level. Ideally, the water level in the tank should be about ½-inch below the overflow tube.

A toilet whose water level in the tank is low will also have a poor/weak flush.

If the water level inside the tank is okay, check if the refill tube is connected to the overflow tube. A refill tube is a small tube connected from the fill valve to the overflow tube.

After flushing, as the fill valve fills the tank with water, the refill tube sends some water down to the bowl via the overflow tube. If the refill tube is detached from the overflow tube, that is the source of your problem.

You will only need to attach it back and flush the toilet. Check the new water level inside the bowl.

If the water level in the tank is low, you will need to adjust it. For more information on how to adjust the water level in the tank and bowl, check out this post.

Sometimes a hairline crack on the bowl can cause the level of water in the bowl to drop. The water may pool at the bottom of the toilet or drain out. If that is the case, you will need to replace the toilet bowl or the whole toilet.

3. Unclog the Plumbing Vent

A plumbing vent, also known as a vent stack is the vertical pipe running through the roof of your house. It is connected to the main house drain stack to remove sewer gases from the drain-waste-vent system and also bring in air into the system.

By bringing in air, the plumbing vent helps fixtures drain faster and quietly, by avoiding creating of negative air pressure. At the same time, sewer gases will also exit the system through it.

If the plumbing vent is clogged, air will not be introduced into the system, and sewer gases/odors will not be removed. As a result, your fixtures (tubs, showers and sinks) will drain slowly and there will be a sewage smell in the bathroom.

Another sign that your plumbing vent is clogged is when the tub/shower/sink drain gurgles when the toilet is flushed. This is due to creating of a vacuum in the drain, causing the water in the drain traps to be siphoned out.

You will also notice your toilet bubbling after being flushed. The bubbles are sewer gases which are being forced out, and will result in a sewage smell from the toilet.

If all these signs are present in your bathroom, a clogged plumbing vent is indeed the problem, although the same could also be caused by a clogged drain stack. Here is how to unclog a vent stack:

  • Grab a ladder and armed with a garden hose climb to the roof of the house.
  • Use the hose to try and dislodge any clog you may find in the vent stack.
  • Have someone on the ground turn on the water. As the water level rises inside the stack, its weight may just be enough to push down the clog.
  • If the above fails to work, upgrade to a drain snake.
  • Hopefully that will remove the clog and ultimately help you get rid of the smell from your toilet.

4. Tighten Toilet Bolts or Replace Toilet Wax Ring

You toilet is fastened to the floor using 2 bolts. The bolts are hooked on the toilet flange (closet flange) which in turn is installed in the drainpipe.

There is a seal called a wax ring between the bottom of the toilet bowl and the top of the flange. The wax ring creates a watertight and air tight seal between the drainpipe and the toilet, ensuring that wastewater and sewer gases do not leak out.

Toilet bolts are used to compress the wax ring tightly between the toilet and the flange. With time, the bolts can loosen or even corrode. If the toilet bolts are loose, the wax ring will not create a proper seal.

Either wastewater will pool at the base of the toilet, or sewer gases will escape through it. Both can also happen.

To check if the above is the situation, grab your toilet and try to rocket it a little. If it is wiggling, that there is the problem.

Toilet bolts are usually covered using plastic caps on both sides of the bowl. Pry off the caps and tighten the bolts using an adjustable wrench.

Check if that fixes the problem.

If the problem is caused by a damaged wax ring, you will need to replace it. Sometimes you may need to replace the toilet flange as well, which if broken causes the toilet to rock, breaking the wax ring seal and hence a sewage smell from the toilet.

For more information on how to replace a toilet tank wax ring and flange, check out this post.

5. Clean the Toilet Tank and Bowl Rim

I am sure you frequently clean your toilet bowl but how often do you clean the inside of the tank? Almost never!

Over time, bacteria may escape from the sewer lines and accumulate under your toilet bowl rim, which can be a cause of horrible smells.

The same can also happen in your toilet tank. Bacteria from your water source can accumulate at the base and sides of the toilet tank resulting in smells, despite your toilet bowl and outside of your tank being clean.

Cleaning the toilet tank and rim of toilet bowl will remove the smell. You will need a lot of white vinegar for this.

This is how to clean a toilet tank and get rid of smells:

  • Turn off water to the toilet tank. The shut off valve is one the wall behind the toilet.
  • Flush the toilet and hold down the trip lever to remove as much water as possible.
  • Remove the toilet tank lid and place it away in a safe place where it cannot fall off and crack.
  • Dump about 2 cups of baking soda inside the tank.
  • Now slowly add vinegar until just below the top of the overflow tube.
  • Pour some baking soda and vinegar down the overflow tube as well. This will break down the gunk inside the rim of the bowl
  • Wait for about any hour, or as long as you can.
  • Flush the toilet to dump the vinegar and baking soda solution.
  • Spray a dish soap all over the inside of the tank.
  • Put on rubber gloves and scrub away the gunk using a brush or sponge.
  • Use a toothbrush to clean tight spaces.
  • Grab a toilet brush and wet it using regular toilet cleaning detergent. Scrub under the rim of the bowl till it is spotless.
  • Turn on water to the toilet and flush it a few times to rinse the toilet.
  • Put the lid back on.

Although bleach can be used to clean a toilet tank, avoid using it as it causes wearing out of rubber parts of the toilet tank like the flapper, resulting in leaks.

And that is how to fix a clean toilet that smells so bad. I hope this guide was helpful.

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