silicone rubber water bottles

How to Remove Mold From Silicone Rubber Water Bottle

Silicone water bottles are durable and easy to clean but aren’t mold-resistant. If you don’t clean or store your bottle correctly, you’ll inevitably expose yourself to some health risks related to drinking moldy water.

But that’s not the end of the world. In this article, we’ll tell you exactly how to remove mold from a silicone rubber water bottle and how to prevent it from growing again. Whether you’ve just discovered a few specks of mold or you’re dealing with a more stubborn situation, we’ll give you all the tips to ensure your bottle is clean, safe, and ready for use. Let’s learn how to banish mold from your silicone rubber water bottle once and for all.

What You’ll Need

Before you get on with cleaning the black spots on your rubber water bottle, you need to gather a few things. Here’s what you might need:

  • Mild Dish Soap: Choose a gentle dish soap, free from harsh chemicals and fragrances.
  • Baking Soda: It’s a natural solution to eliminate mold and mildew stains and odors.
  • White Vinegar: White vinegar is an excellent natural cleaner with antimicrobial properties. It can disinfect your bottle and remove mold.
  • Soft-Bristle Brush or Sponge: You’ll need a soft-bristle brush or sponge to scrub the silicone water bottle interior and exterior.
  • Toothbrush and/or Cotton Swabs: A toothbrush with soft bristles is handy for reaching and cleaning tight spots and crevices in the bottle’s cap and mouthpiece.
  • Boiling Water: It will sterilize your water bottle and help kill any remaining mold spores.

These are all simple items that you probably already have. And if you don’t, it’s a good idea to keep some baking soda, vinegar, and your old toothbrushes for similar situations. These are universal cleaning tools for all surfaces and for removing mold in your thermos.

Cleaning Preparation

Your first task is to prepare your bottle for cleaning. Here’s what you should do:

  1. Empty and Disassemble the Bottle: Pour out any leftover liquid, and if your bottle has a cap or mouthpiece, remove them as well.
  2. Rinse With Hot Water: Rinse the bottle inside and out thoroughly with hot water from the tap. That will loosen any surface mold.
  3. Check for Any Leftovers: Examine the bottle for visible particles that you can remove. Scrub them gently with that soft-bristle brush or sponge. Don’t worry if you can’t remove all of them — this is just the first step. 

These steps will help you evaluate the situation and ensure thorough cleaning.

How to Remove Mold From Silicone Rubber Water Bottle 

You can try different methods for removing mold from your silicone water bottle, depending on what you have at home and how bad the damage is. Here are the three most commonly used methods:

Method 1: Soap & Water

It’s a gentle yet effective method for removing mold from silicone rubber water bottles. This method is ideal for mild to moderate mold infestations.


  1. Prepare the Cleaning Solution: Fill a container large enough to fit your water bottle with warm water and add a few drops of mild dish soap to it. Mix until you get a soapy solution.
  2. Scrub the Bottle: Put the silicone rubber water bottle in the soapy water. Use a soft-bristle brush or sponge to scrub the bottle inside and out, paying extra attention to areas with visible mold. Don’t put too much force in it to avoid damaging the silicone.
  3. Scrub the Rubber Seal: You can remove the black mold on your water bottle seal by scrubbing it gently with the toothbrush or cotton swabs. Again, be thorough but gentle.
  4. Rinse and Dry: Rinse the bottle thoroughly with clean, warm water to remove any soap residue. Let the bottle air dry completely before reassembling and using it again.

Pay attention to that last step. If you don’t let the bottle air dry completely, mold will easily grow back in. I’ve made this mistake at least several times before I learned my lesson. 

person holding a black silicone water bottle

Method 2: Baking Soda Paste

This is hands down my favorite solution. It’s natural, easy, and effective. 


  1. Mix Baking Soda and Water: In a small bowl, mix baking soda with a small amount of water to create a thick paste.
  2. Apply the Paste: Apply a generous amount of the baking soda paste to all places with black gunk in the water bottle.
  3. Scrub and Wait: Scrub the paste into the mold stains with a brush or sponge. Let it sit for at least 15-20 minutes or overnight. This allows the baking soda to break down the mold.
  4. Scrub Again and Rinse: Scrub the mold-stained places again.
  5. Rinse the Bottle: Use warm water to remove the baking soda and any mold residue.
  6. Air Dry: Wait until it’s entirely dry before using it again.

Method 3: White Vinegar

White vinegar is a natural disinfectant and mold remover that can effectively eliminate mold spores and odors from your silicone rubber water bottle.


  1. Mix White Vinegar and Water: Use equal; amounts.
  2. Soak the Bottle: Soak your water bottle for at least 20-30 minutes in the vinegar solution to kill mold spores.
  3. Scrub the Mold: Scrub gently but thoroughly in all affected areas.
  4. Scrub the Mouthpiece: If you notice mold in the water bottle mouthpiece, use a toothbrush or cotton swabs to scrub the place. 
  5. Rinse & Dry: Rinse thoroughly with warm water and let it air dry completely.

Whatever method you choose, scrub well and be patient. Still, I recommend the baking soda if you have it at home.

Can You Use the Dishwasher to Clean the Mold From a Silicone Water Bottle?

Generally, you can put silicone in the dishwasher, as long as it’s labeled as dishwasher-safe. However, not all silicone rubber water bottles are dishwasher-safe, and the heat inside can potentially damage the bottle over time. Also, there’s no guarantee that the dishwasher will reach all those crevices where mold grows in a bottle. 

If your bottle is labeled as dishwasher-safe, you can consider it for occasional cleaning. Still, I’d recommend scrubbing it yourself if you want to remove mold and mildew from a rubber water bottle.

How to Sterilize the Bottle

If you want to ensure your water bottle stays free from bacteria and any remaining mold spores, you can sterilize it as a last step in the cleaning process. Here’s how to proceed:

  1. Disassemble the bottle. 
  2. Boil water in a pot large enough to fit your bottle. 
  3. Put all bottle parts fully into the boiling water.
  4. Boil for 5–10 minutes. This will kill bacteria and sterilize the bottle.
  5. Carefully remove the water bottle components from the water with tongs or oven mitts.
  6. Let the components cool down naturally. Rinsing them with cold water might cause damage due to the temperature change. 

While boiling water is an effective method for sterilization, it may not remove stains or discoloration from mold or other substances. For stubborn stains, use the methods above to remove mold on the rubber seal water bottle. 

How to Prevent the Mold From Growing on Your Bottle Again

Removing mold from your silicone rubber water bottle is useless if you don’t prevent it from growing again. Here’s how you can do that:

  • Clean your bottle regularly. It’s best to do it at least weekly. 
  • Let your bottle dry completely. Mold grows in damp environments, so keeping your bottle dry when not in use will prevent that. 
  • Avoid putting juices or sports drinks in your water bottle. Mold is more likely to grow if you use the bottle for sugary or acidic drinks
  • Store your water bottle with the cap off for better ventilation and preventing moisture buildup inside.
  • Store the water bottle in a cool, dry place when not in use to discourage mold growth.
  • Examine your bottle for signs of mold regularly. Catching it early will prevent you from more serious damage. 

Unfortunately, even reusable water bottles have a lifespan. If you cannot clean your bottle no matter what you’re doing, consider switching to a new one. But before you do that, you can try switching any damaged components, like the rubber seal. Damaged components can create spaces where mold can thrive. You can find rubber seal replacements on Amazon.


Does bleach damage rubber seals?

Yes, bleach can damage rubber seals over time. It’s a strong chemical that can cause the rubber to deteriorate and lose its elasticity, potentially leading to leaks. It’s best to use milder cleaning methods for rubber seals.

Does vinegar damage silicone?

No, vinegar doesn’t damage silicone. It’s a safe and effective cleaning solution for your silicone water bottle. However, it’s essential to dilute the vinegar with water to prevent discoloration or a lingering vinegar smell.

Will 100% silicone grow mold?

No, 100% silicone is resistant to mold growth because it doesn’t provide a food source for mold. However, mold can still grow on dust or debris that may accumulate on the silicone surface, so you should clean the item regularly.

How long does it take for silicone mold to go away?

Getting rid of silicone mold depends on the mold and the cleaning method. With effective cleaning and disinfection, you can remove the mold in a matter of hours to a few days.

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