How to Clean a Stained and Smelly Toilet


Grab some common household products to get your toilet bowl clean and fresh, no matter how badly it’s stained.

Keeping your toilet clean is vital to good health. Dirty toilets harbor all sorts of bacteria and viruses. Thanks to “toilet plume” — tiny droplets spewed with every flush — these germs spread to nearby surfaces. That’s why, if one person in your home gets a stomach bug, everyone else seems to catch it, too.

A dirty toilet makes your entire bathroom smell bad, too. Sometimes, the odor reaches even farther. And who wants to open the lid to find a yucky green, orange, or rust-colored stain in a toilet they’re about to use?

Fortunately, it doesn’t take a lot of harsh chemicals to get your commode fresh and clean. Read on for how to use common household ingredients to clean your toilet and remove stains.

Before You Start

There are a couple of safety precautions you must take before you begin cleaning your toilet.

1. Take out automatic toilet bowl cleaners. It’s never safe to combine toilet cleaning products. So, if you use a toilet tank additive, remove it before cleaning your toilet. Of, if you use a continuous-clean toilet bowl gel, scrape it away with a rubber spatula. Then flush your toilet twice to rinse away any residue from these products. (See also, Cleaning Products You Should Never Mix.)

2. Run the fan. Cleaning your dirty toilet releases bacteria into the air. Use your bathroom exhaust fan or open the windows to cut down on how much you breathe in.

Grab some common household products to get your toilet bowl clean and remove stubborn toilet stains. 
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Toilet paper and bowl brush next to open toilet in minimalist bathroom

How to Clean a Stained Toilet Inside and Out

Follow these steps to clean your dirty toilet and get rid of stains using the homemade toilet bowl cleaner.
Time Required30 mins
30 mins
Total Time30 mins


  • Toilet brush
  • Old toothbrush
  • Cleaning rags or paper towels


To Clean Outside of Toilet

To Clean Inside of Toilet

To Clean Toilet Stains


How to Clean the Outside of Your Toilet

  • Remove everything. Take any spare toilet paper or loo rolls, magazines, and other decorative objects off the toilet tank. If you use a lid cover, pull that off, too. You'll be spraying cleaning products, so remove stuff on the floor near the toilet as well.
    Toilet paper and bowl brush next to open toilet in minimalist bathroom
  • Wipe with a dry cloth. Disinfectants work best on clean surfaces. Too much dirt or other grime overloads them and reduces their germ-killing abilities. So, use a dry rag or paper towel to wipe the toilet tank, lid, seat, and pedestal to start.
  • Treat Seat Stains. Use the corner of a damp cleaning rag and a little baking soda to clean stains and spots on the toilet seat. Wipe with a clean, damp rag before proceeding.
  • Spray with disinfectant and wait. Lift the toilet seat and spray the rim of the bowl with disinfectant. Spray the hinges, too. Put the seat down and spray it and the underside of the lid. Close the lid and spray the rest of your toilet's exterior.
    It's important that you don't start wiping right away. Disinfectants need time to work. Wait the amount of time indicated on the product's label. Or, if you're using my homemade bathroom disinfectant recipe, wait 5 minutes for it to work.
  • Scrub the hinges. Toilet seat hinges get covered with grime, especially if you're potty training kids. Scrub them with an old toothbrush after applying the disinfectant. (You may need to pop the covers.)
  • Wipe top to bottom. If you're using the homemade bathroom disinfectant, wipe it with a dry cloth or let it air dry. For store-bought disinfectants, check the product label to see if you need to rinse it with water. Either way, wipe the tank, handle, lid, seat (both sides), rim and pedestal.
    Overhead view of hands in rubber gloves using a sponge to clean rim of dirty toilet
  • Flush. You must flush your toilet after cleaning the exterior to remove any cleaning product in the bowl. Urine may cause a dangerous chemical reaction with bleach-based cleaners if you don't. Repeat these steps at least once a week.

How to Clean Your Toilet Bowl

  • Empty it. The less water in your toilet bowl, the better you'll be able to clean it. So, turn off the water at the supply hose by twisting the oval-shaped stop valve to the right until it stops. Or, open the lid of your tank and slide a wooden spoon beneath the float lever to keep it from moving. (This works well if you can't find the supply valve, or it won't turn easily.) Then, flush the toilet to drain the bowl.
    Inside view of toilet mechanism with instructions to slide wooden spoon under float lever
  • Loosen buildup. Add 1-2 drops of tea tree or other antibacterial essential oil to the water in the bowl. (Optional.) Then, dip your toilet brush into the water to get it damp. Sprinkle the end of the brush with baking soda and use this to scrub under the rim of the bowl. Work your way down the walls and into the drain as far as you can. Do not flush.
  • Activate. Spray or pour vinegar into the toilet bowl, starting under the rim. This will cause fizzing and foaming that helps lift away stains while killing germs.
  • Wait. Let the vinegar sit in the bowl until the foaming stops — about 5 minutes.
  • Scrub. Using the toilet brush, scrub under the rim and work down the sides of the bowl into the drain.
    Closeup of hands in rubber gloves using sponge and brush to clean inside toilet bowl
  • Refill. Turn the toilet water supply's stop valve to the left, so the tank refills with water. (Or remove the wooden spoon from blocking the float lever.) Go ahead and leave the end of your toilet brush in the bowl while it refills.
  • Flush. Once the toilet bowl is full of water, swish the brush around to rinse it and then flush. Repeat this weekly to keep your toilet bowl smelling fresh and clean.

How to Clean Toilet Bowl Stains

  • Identify the cause of toilet stains. Orange stains at your toilet's waterline occur due to mildew. Scrubbing it using the steps above removes them.
    Gray, black, or green stains at the waterline are due to hard water buildup. Rusty grime below the waterline is bacteria clinging to mineral buildup. So are those orange streaks running from the rim to the water. Scouring your toilet bowl the right way removes them.
  • Empty. Shut off the toilet's water supply and flush to drain the bowl.
  • Mix a homemade toilet bowl stain remover. In a cup, combine 1/2 cup Borax with 1 tablespoon of white vinegar. Add more vinegar if needed to make a paste — but don't make it too runny.
  • Apply. Using a rag, apply the paste to the toilet bowl stains and scrub by hand. Wait 5-10 minutes then scrub with the brush. Use more homemade bowl cleaner as needed until the stains are gone.
  • Clean the toilet rim holes if needed. Sometimes the water jet holes under the toilet rim get clogged. When this happens, the bowl fills slowly and doesn't entirely flush. The clogs are buildup from either bacteria (black or orange) or mineral buildup (light or green).
  • Unclog. To clean the toilet rim holes, use an old toothbrush and the homemade toilet bowl stain remover, above. Work the toothbrush over each hole to work the cleaner in there. You can insert and rotate the end of a pipe cleaner for very stubborn clogs.
  • Rinse. Turn the water supply back on and wait for the toilet to refill. Dip the toilet brush in the water, scrub the walls of the bowl and under the rim to loosen the stain remover, and flush.

Common Questions about Cleaning Toilets

Below are some frequently asked questions about cleaning dirty toilets and their answers. Remember, when it comes to cleaning your home, just because something can work doesn’t mean it’s a good idea. You also need to think about the risk of long-term damage.

A fast cleaning hack might save you time, but if it winds up costing you a lot of money to repair, it’s not worth it.

How do I clean my toilet brush?

No matter what method you use to clean the toilet bowl, don’t put the brush away dirty and wet. Tap it against the edge of the toilet bowl to shake off as much moisture as possible. Then, spray it with disinfectant until it’s wet. Let it air dry propped under the toilet lid. Once it’s dry, put it back in the holder.

Should I use a pumice stone on toilet stains? Or sandpaper?

This is a perfect example of something that can work but which will cost you more time and money in the long run. Both pumice stones and sandpaper are very abrasive. Toilet bowls are porcelain. Using a strong abrasive on porcelain will, indeed, remove surface stains. It will also ruin the slick finish that keeps toilet stains from becoming permanent. Then you’ll wind up with more toilet stains more often, and they’ll be even harder to remove.

Can I just pour bleach into my toilet to get rid of stains?

Sometimes. A half-cup of bleach poured into the bowl can remove stains below the waterline in 5 minutes. But it won’t do anything for stains above the waterline, like orange lines streaking from the rim. It also won’t remove mineral buildup or limescale. So, you might need to follow the directions above anyway.

Can I use a can of Coke to clean my toilet?

Coca-Cola is very acidic. Many people have had luck pouring a can into the toilet bowl and letting it sit overnight. After a quick scrub and flush the next morning, they say the stains are gone. I haven’t tried it, to be honest, because it seems like I’d just be inviting ants to a feast.

Can I use WD-40 to clean my toilet?

WD-40 is a mineral oil-based spray. It’s fantastic at silencing squeaky hinges or loosening tight screws. It can help loosen rusty residue in toilet bowls, but that doesn’t mean it’s a good approach. Most counties forbid pouring mineral oil down drains because it winds up in the water supply. That’s why you shouldn’t flush it, either.

Can I use Downy or fabric softener to keep my toilet smelling fresh?

There’s a “cleaning hack” circulating on Pinterest and in some Facebook groups, which suggests adding a fabric softener like Downy to the toilet tank. The idea is that it’ll freshen the bowl with every flush. But, this is another cleaning hack that can cause damage, and it doesn’t work well. The ingredients in the fabric softener can damage your toilet’s flapper seal. Then your commode won’t flush properly and is likely to keep running. Besides, flushing releases all but one or two inches of water from the tank, so you’d just be flushing pricey fabric softener down the drain. Literally.

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  1. What about tips for cleaning the tank? That’s where my toilet is dirty and smells

    1. Katie Berry says:

      Hi Tina,

      I’d shut off the water supply at the wall and empty the tank. Then, use a sponge or towel to get out as much water as you can. (Be careful you don’t damage the mechanisms.) Go over both sides of the flapper and its gasket with a damp microfiber cloth and a little baking soda to remove grime, then wipe it clean. Use the toilet bowl stain remover on any stains you find. Wipe away as much of the paste as you can before refilling the tank, so you aren’t leaving stuff in there that can clog the flushing mechanisms. Once you’ve got it all out, turn on the water supply to fill the tank and flush a few times.

  2. 4 stars
    What if you’ve done all this and you still cant kick that urine smell from little boys?

    1. Katie Berry says:

      Hi Kristin,

      Boy pee doesn’t smell any different to girl pee. But boys are a lot messier when they’re young. So, if you’ve done all this and still get that whiff of urine odor, try cleaning these areas, too:

      1. The walls behind and around the toilet. Soap and water with a small amount of baking soda stirred in should do the trick.

      2. The floor at the base of your toilet, including the caulk around the toilet pedestal. Get these areas damp and sprinkle them very lightly with baking soda. Let that sit for a few minutes to deodorize then wipe it away with plain water. Follow that with whatever floor cleaner you ordinarily use. (Here’s my homemade floor cleaner if you want to try it.)

      3. Scrub the toilet seat hinges with baking soda and water. In fact, you might want to replace your toilet seat every 6 months or so while they’re learning.

      Best of luck!

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