Help! What Should I Do If My Clean Toilet Smells Like Urine?

Updated February 16, 2022
A mother washing her hands next to her daughter
Photo: kate_sept2004 / E+ / Getty Images


  • Use bleach to break down organic compounds.

  • Replace a faulty toilet wax ring to prevent bacteria from breeding.

  • It costs less than $200 to replace a toilet flange.

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If you find yourself slapping on a respirator every time you pass the bathroom door, it’s time for action. You probably know all too well that stubborn bathroom odors can linger, no matter how much you clean or how many warm vanilla candles you light. Thankfully, you just have to have the right strategies for disinfecting your bathroom and attacking those odors when your toilet smells like urine.

1. Bleach, Bleach, Baby

Detail of a man’s hand in gloves cleaning a toilet
Photo: Wattanaphob Kappago / EyeEm / Getty Images

Unless you’re using the right cleansers, you’re not going to succeed in sending the pee fumes packing. To get rid of urine odor, you’re going to need bleach to break down the organic compounds that make urine odors so stubborn and so stinky. 

But it’s not going to be a slap-dash operation—you’re going to want to clean not just at the bullseye of the toilet, but all around, covering a far larger area and far more surfaces than you probably expect. This means cleaning more than the toilet: the floors, the walls, the cabinets, the toilet tank, under the toilet rim, etc.

Remember, as much as you might not like to think about it, those nasties can splash, and accumulate, pretty much anywhere and everywhere. So you’ll need to grab your bleach—pronto!

2. Seal the Deal

If you’ve given your bathroom a thorough bleaching, but you find those pesky urine odors still lingering, then it may mean you’ve got a problem with your toilet wax seal. 

Wax seals are generally built to last, but they’re by no means foolproof. And if you get a crack or if the seal begins to pull away from your floor or your toilet base, then that’s the perfect place for urine to accumulate and breed bacteria.

If your toilet wax ring fails, then your only choice, really, is to replace it. If you’re handy and have the time, inclination, and muscle to remove and then reset your toilet, then you can probably replace the toilet wax ring yourself in a single afternoon.

3. Face the Flange

A white toilet in a clean bathroom
Photo: onurdongel / iStock / Getty Images

Your toilet wax ring might not be the only issue, however. You might also have a cracked, broken, or otherwise failing toilet flange. And that could mean that urine is accumulating and reeking from the base of your toilet and that sewer gas fumes are rising and escaping through the flange. Yikes!

Just like with the wax ring, if your flange breaks or has started to fail, you’ll need to replace it. Unless you have a lot of plumbing experience, though, you’ll probably want to leave it to the professionals. They’ll have the tools, training, and experience to get the job done fairly easily and at a relatively low cost, generally for less than $200

Most importantly, a local plumber will be able to check for potential water damage in your subflooring. If your flange has leaked and caused water damage in the subfloor, repairing it immediately—while the toilet is disconnected—will prevent further damage and additional time and money spent on repairs down the road. Plus, you’ll get rid of those saturated, odor-producing boards that are keeping you from the fresh bathroom-slash-home-spa you’ve got your heart set on.

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