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How to Clean a Toilet Tank

Mold and rust stains inside your toilet tank can be cleaned away when you use the right products and technique for each stain. Learn how to treat them differently and ensure you get the best results.

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By Mary Gagliardi
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It’s just not as effective to clean toilet tank mold or rust without draining the tank and scrubbing because a tank full of water will dilute cleaning products too much, reducing their cleaning power. Instead, take a little time to pre-clean your rust or mold stained toilet tank with scouring powder first before cleaning the actual stains and improve your results. If your toilet tank has both mold and rust stains, clean the rust stains before dealing with the mold stains.

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Rust from the water supply

Rust stains in the toilet tank indicate a problem with the water supply

When rust accumulates in toilet tanks, even if you clean away the rust it will probably come back. Installing a water filtration system for the home water supply that removes iron from the water can help prevent the problem from reappearing. 

Pre-clean first with cleanser

Scrubbing with cleanser first jumpstarts stain removal

Plumbing restoration experts recommend scouring the inside of a rusty or moldy toilet tank with scouring powder before tackling any stains.

Clean rust stains before mold stains

When you have both stains, which one you treat first matters

Bleach is highly effective at removing mold stains, but will actually make rust stains worse. When your toilet tank has both rust and mold on the tank interior, clean the mold stains only after using a rust remover for the rust stains to get the best performance out of both products. 

Important safety reminder

Never mix strong acids and bleach together

Rust remover products are strong acids — that’s why they are effective — but they can never be mixed with Clorox® Bleach or any other sodium hypochlorite bleach products because hazardous gas can be released that may be fatal. Make sure you thoroughly rinse the tank in between different treatments so you don’t inadvertently mix chemicals. 

Gather your supplies

  • Clorox® Disinfecting Bleach with CLOROMAX®
    Clorox® Disinfecting Bleach with CLOROMAX®
  • Bleach-free scouring powder (like bon ami or barkeeper’s friend)
    Bleach-free scouring powder (like bon ami or barkeeper’s friend)
  • Rust remover – available at hardware stores
    Rust remover – available at hardware stores
  • rubber gloves
    Protective gloves
  • Safety glasses
    Safety glasses
  • Heavy duty scrubber sponge
    Heavy duty scrubber sponge
  • measuring cup
    Measuring cup
  • Plastic cup
    Plastic cup
  • Small nylon brush
    Small nylon brush
  • test strips
    pH test strips

Steps to pre-clean a toilet tank with scouring powder

  1. 1

    Open windows to improve ventilation

    Start by opening windows to allow good air circulation in the area you’re cleaning. For rooms without windows, you can also use a fan to improve air circulation.

    open window with curtains
  2. 2

    Drain the toilet tank

    Remove the tank lid and turn off the water supply at the back of the toilet before flushing the toilet. Hold the handle down so the tank drains completely, then check to make sure the flapper is closed and the bottom of the tank is sealed.

  3. 3

    Pre-clean with scouring powder

    Sprinkle some scouring powder onto the sponge and then dampen it with a little water. Use this to scrub the sides and the bottom of the tank.

    Tip

    Wear gloves and safety glasses when cleaning inside the toilet tank.

  4. 4

    Rinse the tank

    Use the plastic cup to rinse the tank by pouring clean water down the sides of the tank. Hold the handle down while you do this so the scouring powder is rinsed from the tank into the toilet bowl. Turn the water supply back on so the tank fills, then turn the water supply off again and flush the toilet to empty the tank and clear any remaining scouring powder from the toilet bowl.

Steps to clean rust in a toilet tank

  1. 1

    Start with a pre-cleaned and rinsed toilet

    Cleaning with the scouring powder first will reduce the amount of stain you have to deal with, so don’t skip the pre-clean steps. After completing the pre-cleaning steps, you will have a rinsed empty toilet ready to go.

  2. 2

    Apply the rust remover

    Squirt the rust remover product directly onto the stains inside the toilet tank, scrubbing them with the nylon brush. For severe stains, reapply the rust remover and continue scrubbing as needed.

    Tip

    Read and follow the instructions on the rust remover product, including wearing heavy duty protective gloves and safety glasses.

  3. 3

    Rinse the tank

    Use the plastic cup to rinse the tank by pouring clean water down the sides of the tank multiple times to completely rinse away the rust remover. Hold the handle down while you do this so the flapper is up, allowing the rust remover to be completely rinsed from the tank. Turn the water supply back on so the tank fills.

  4. 4

    Check the pH of the water in the tank

    Use a pH test strip to check the pH of the water in the tank. It should be a neutral pH of 7 or at least the same pH as the water coming from the faucet. If the pH is lower than the water from the faucet, there is still rust remover in the tank, so repeat the rinse step then retest. Once the water in the tank is a neutral pH, flush the toilet one final time, emptying the tank completely to ensure any residual rust remover is rinsed from the toilet bowl and all the way through the p-trap into the waste line.

    chlorine test strips

Steps to clean mold from a toilet tank

  1. 1

    Start with a pre-cleaned and rinsed toilet

    Cleaning with the scouring powder first will reduce the amount of mold you have to deal with, so don’t skip the pre-clean step. After completing the pre-cleaning steps, you will have a rinsed empty toilet ready to go.

    Tip

    You do not need to pre-clean with scouring powder again if you already did before using any rust remover, but you will need to empty the tank before mixing up the bleach and water solution.

    Never mix strong acids like rust removers and bleach together as hazardous fumes will result that can be fatal.

  2. 2

    Make the bleach and water solution in the tank

    Check to make sure the flapper at the bottom of the empty tank is closed, then use the measuring cup to add 1 gallon (16 cups) water to the tank. Then add 1/3 cup Clorox® Disinfecting Bleach to the water in the tank.

    bleach pouring from bottle
  3. 3

    Scrub the inside of the tank

    Use the scrubber sponge to wipe the bleach and water solution onto the sides of the tank, reapplying the bleach solution as needed to keep the surface wet for 10 minutes and scrubbing as needed.

  4. 4

    Rinse the tank

    Use the plastic cup to rinse the tank by pouring clean water down the sides of the tank multiple times to completely rinse away the bleach. Hold the handle down while you do this so the flapper is up and the rinse water and bleach can drain out of the tank. Turn the water supply back on to fill the tank.

  5. 5

    Flush the toilet

    Flush the toilet one more time to make sure no bleach solution remains in the toilet bowl.

Frequently asked questions

Can I use toilet bowl cleaner to clean the inside of my toilet tank?

No — this is not recommended. Toilet bowl cleaners are designed to work on the porcelain surface of the toilet bowl, not the inside of the toilet tank. Toilet tablets, however, are a good option because they are designed to use inside the toilet tank. For long lasting cleaning of a toilet tank and toilet bowl, try Clorox® Automatic Toilet Bowl Cleaner tablets.

What can I put in my toilet tank to make it smell better?

Try Clorox® Automatic Toilet Bowl Cleaner Bleach & Blue toilet tablets, which have a fresh Rain Clean® fragrance.

Can you put bleach in a toilet tank?

Yes — when used as directed, bleach can be used to clean mold off the inside of a toilet tank.