Why Does My Toilet Smell Like Urine?

Stubborn urine odors can make even the nicest bathroom feel like a dump.  Bathroom odors have a tendency to linger, regardless of how often and how well you clean or how many air fresheners you use. Getting rid of the urine smell in your toilet requires the right disinfecting strategy to get rid of the smell for good.

Why Does it Smell?

There are really only a few reasons your toilet smells like urine.  First, it’s not clean, or at least not really clean. The next is that your toilet is clean, but the urine smell originates from another surface in your bathroom that has pee on it. 

The other reasons don’t involve bathroom hygiene. Instead, the urine smell could be coming from the failure of one or more parts of your toilet seal, the part of your toilet that attaches to the bathroom floor.

Use a Black Light to Find The Source

A small black light in a dark bathroom does wonders for helping you locate the pee spots you missed. Once you have located the problem area, use some of the suggestions below to combat the smell.

Ways to Get Rid of the Smell


If you’re not using the right cleaners, you won’t send your urine smell packing. We’ve written about bleach before as it relates to clogs, but it can also work wonders for combating the urine smell. To get rid of urine odors, you need to use a cleaner that contains bleach.  Bleach breaks down the organic compounds that cause urine smells to be so bad and hard to get rid of.

Unfortunately, if your toilet already has a lingering urine odor, it’s not going to be a quick clean job.  You want to clean all around the toilet, not just the toilet itself, and clean more surfaces than you think you need to.  This means using a bleach-containing cleaner to clean the floors, walls, cabinets, toilet tank, and every surface on or near your toilet.

We don’t like to think about it, but pee splashes if you have men or boys in your house. So, naturally, this leads to the accumulation of urine particulars pretty much everywhere in the bathroom.  So, grab your bleach bottle and rubber gloves and get to work.

Use an Old Toothbrush to Help Clean Around the Toilet Base

Small amounts of pee are guaranteed to have crept their way into the small crack at your toilet base.  If it’s been there for a while, it will be yellow goo that is hard to clean.  A plastic knife can also work well to clean out small cracks.

Clean Fabric Surfaces

Spray fabric surfaces in your bathroom with Urine Out Pet Odor Remove or vinegar and water to remove any lingering smells after you’ve done a thorough cleaning.

Washing the Molding

We mentioned washing your walls but clean the molding at the same time. Urine dries underneath molding on the walls, so your toothbrush or plastic knife will come in handy for cleaning small crevices. Also, making everyone flush with the seat closed can help reduce splashing in the future. 

Be Aware of Laundry Baskets, Step Stools, and Garbage Cans

If you’ve run out of sources for the smell, check these common culprits.  If it’s in your bathroom, it’s potentially been sprayed.

If you have little boys who stand on a stool to reach the toilet, they have likely missed the bowl a few times and hit the stool. Keeping garbage cans and laundry baskets in the bathroom to those made of plastic will make them easier to clean long-term and less likely to retain odors.

This is especially common the closer these items are to the toilet bowl itself. Make sure that there is ample room around the bowl so that other items like this stay urine-free.

Wash the Bath Rugs

If you have a bath rug in front of your toilet to save your floor, wash it regularly. This is a common problem spot when it comes to smell. The thicker the carpet itself it, the more often you want to wash it. This will help prevent the urine getting too deep and engrained into the rug itself.

Sealing the Deal

If you’ve given your bathroom a total bleach scrub down and it still smells like urine, the problem may lie in your toilet’s wax seal.

Wax seals are designed to last a long time, but they’re not perfect. For example, a crack in the seal or the seal pulling away from the floor or toilet base provides the perfect spot for urine to accumulate and start a colony of bacterial growth.

Once the wax seal on your toilet fails, your only option is to replace it with a new one.  If you’re relatively handy and have some muscle to lift off your toilet, this is a job you can do yourself in a couple of hours.

The first step to replacing a wax seal on a toilet is to shut off the water.  Turning off the main water source is the safest option, but you can turn it off right at the toilet if you have an available shutoff.  The next step is to unbolt the toilet and take it off.  The wax seal is easy to see once you have the toilet off.

Remove the old wax seal thoroughly.  This might mean using a scraper or a knife to take off excess bits that are stuck down.  Replace the new seal and bolt the toilet back into place. 

Lifting toilets on and off is not easy, as they’re heavy and will break if you drop them, turning your simple DIY job into a more expensive and labor-intensive project.  It’s best to get some help for toilet lifting.

Facing the Flange

The wax ring on your toilet may not be the only problem.  Your toilet flange can also become cracked or broken.  Again, the result is a lingering urine odor coming from the base of your toilet that you can’t clean away.  In the case of a broken toilet flange, urine smells and sewer gas are escaping.

A failed toilet flange has to be replaced, just like a wax ring. But, unlike a wax ring, this is probably a job best left to a plumbing professional unless you’re experienced with the process.  The good news is it’s a relatively easy job that can be completed in an afternoon, usually for less than $200.

If you’ve gone so far as to hire a plumber, have them check for water damage on your floor and subfloor while they have your toilet removed. 

Once your flange starts leaking, it leaks water that can cause extensive damage if it gets under your flooring.  If damage is found, the subfloor should be repaired immediately to avoid further repairs in the future.  Removing the damaged flooring will also help you remove any odors that have soaked into the wood.

Worms and Drain Flies

It’s a common rumor that worms in your toilet will cause it to smell bad. Is there truth to this, or is it an old wives’ tale?  It’s not a good sign if you have actual worms in your toilet, but they won’t cause it to smell like urine.  It’s more likely for another insect to be the culprit.

One nasty tiny insect that might cause your toilet to smell is a drain fly. These bugs look like fuzzy versions of a moth, but they’re small.  They like to breed in wet areas like sink and toilet pipes during warm weather.

The smell exhibited by drain flies sometimes smells like urine, but it can also smell like something resembling vomit.  Whichever odor your nose recognizes, they’re stinky. They’re completely harmless to humans, but you don’t want to leave these flies living in your bathroom. They smell bad, and they reproduce like crazy. So, if you think you have drain flies, it’s essential to deal with them as soon as possible.

It’s highly unlikely that you will see the drain flies themselves.  What is likely is that you will spot black worms in your toilet – except they’re not worms, they’re drain fly larvae that gather around openings in sinks and drains.  So now you know.  If you have worms (drain fly larvae) in your toilet, it smells terrible and could be the cause of your lingering urine smell. 

Ridding your toilet of drain flies is relatively simple.  Simply pour a scoop of baking soda, salt, and white vinegar down the toilet.  Let the toilet sit overnight, then pour a pot of boiling water into it.  After you’re done, use a metal brush (preferably one you’ll throw away after) to scrub the inside of the toilet and drain to ensure all the flies and larvae have been killed.

The Bottom Line

If your toilet smells like urine, it can be a sign you missed something when cleaning the bathroom, a sign of a toilet seal failure, or a drain fly infestation.  Any of these things can cause a lingering urine smell.  Realistically, however, the most common cause of urine smells in a bathroom is a bad aim.

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