How to Clean the Rubber Seal on a Water Bottle

Man lifting the rubber seal of his water bottle

A reusable water bottle helps you hydrate while saving the environment. However, bacteria from moisture and saliva can build up on the cap's rubber gasket over time. We're listing several ways on how to clean the rubber seal on a water bottle to ensure you can drink safely.

How to Clean the Rubber Seal on a Water Bottle

To clean a water bottle's rubber seal, you can scrub it using a soft bottle brush, soapy water, vinegar, baking soda, or hydrogen peroxide. You can also soak the rubber in boiling water to loosen the dirt. Rinse and dry thoroughly to prevent grime and mold from growing again.

How often do you wash your Hydro Cell water bottle? Do you pay attention to the rubber seal? Hydro Cell bottles include rubber gaskets in the cap to create an airtight seal, ensuring your drinks won't leak.

Surfer carrying both his board and Hydro Cell water bottle

While you can clean a stainless steel bottle or disinfect it from time to time, there may be instances when you might miss cleaning the cap's rubber gasket. Follow these tips to prevent bacteria from transferring from the rubber to your water.

Soak and Scrub Using Liquid Soap

One of the easiest ways to clean the rubber seal on a water bottle is to scrub it with warm water and a liquid dishwasher. Cleaning the cap and rubber also eliminates odor from beverage residues.

Stachybotrys chartarum, or black mold, is among the most toxic species of mold. If you're not cleaning your drinking bottle properly, the bottle's dark, damp environment will invite mold to grow and settle down.

The warmer it gets, the more likely mold will grow. Organic matter, residue from sweet and salty drinks, and even your cavities provide enough food for fungi and bacteria to grow on rubber seals.

  • Fill your sink with two tablespoons of dish soap and a scoop of warm water. Make sure to check if the soap is safe for silicone or rubber.
  • Soak the cap, especially the rubber gasket, on the water for at least 10 minutes.
  • Use a bottle brush to clean the corners, then scrub thoroughly.
  • Rinse the cap, then let it air dry. You can also wipe it before using the lid again.

Apply a Baking Soda Paste

While you can keep water in a stainless steel bottle for a while, microscopic pests thrive in wet environments like moist rubber seals. Cleaning them with baking soda is another way to prevent unwanted bacteria from living in your bottle, whether it's a stainless steel or glass bottle.Hand showing off a Hydro Cell water bottle

Baking soda is a gentle abrasive, so it's safe to use on rubber gaskets. It also has purifying and deodorizing capacities to remove odor in the cap and water bottle.

  • Combine two tablespoons of baking soda and a bit of water until you form a paste. You can also add dish soap as reinforcement.
  • Use a soft cloth to apply the paste into the creases of the seal.
  • Leave the paste on the rubber for 10 to 15 minutes.
  • Use a bottle brush to scrub the rubber seal and get into the crannies.
  • Wash with soap and warm water before rinsing thoroughly.
  • Let the cap sit overnight or dry it with a dishcloth.

Clean With Vinegar

You may unconsciously prompt the growth of dirt in rubber gaskets. Take bringing water on a hike, for example. Your sweaty skin would touch the bottle's mouthpiece. When you put back the lid, you're also transferring the dirty moisture to the rubber seal.

Fortunately, white vinegar can kill 82% of mold spores and other bacteria species in high-touch items such as bottle lids. As a common household item, vinegar is one of the most convenient cleaners you can use to clean the rubber seal as well as the bottle.

However, vinegar is a byproduct of fermented ethanol, naturally producing acid. Use vinegar sparingly as it may also cause some synthetic seals to stain or deteriorate.

  • Soak the bottle lid and rubber seal in two cups of vinegar.
  • Use a small brush to get into the nooks.
  • Wash with soap and warm water.
  • Rinse thoroughly to remove the vinegar's smell and taste.
  • You can also prepare one-part vinegar and four-parts water in a spray bottle so that you can bring a cleaner anywhere you go.Man lifting the rubber seal of his water bottle

Use Hydrogen Peroxide

In some cases, there may still be a bit of dirt or mold left in the rubber seal even after doing your usual bottle cleaning routine in the dishwasher. You can use hydrogen peroxide as a reinforcement to clean the rubber.

Hydrogen peroxide is another cost-effective and non-toxic cleaner. More than that, its oxidizing properties can act as a disinfectant, deodorizer, and degreaser.

  • Pour 1/4 cup of 3% hydrogen peroxide into a bowl.
  • Put the bottle cap in the bowl, thoroughly soaking the rubber seal.
  • Let the rubber soak for 15 minutes, then give it a vigorous shake.
  • Use a clean cloth to wipe away dirt.
  • Spray some more if there's dirt left, then continue wiping.
  • Rinse with water, then let dry.

Clean With Hot Water

Some cap designs are prone to germ clots. Whether you're using a 32-ounce or 40-ounce water bottle, mildew and dirt will stay in the rubber seal if not cleaned properly. Another cleaning option is to soak the rubber seal in boiling water. 

According to the World Health Organization, hot water ranging from 140-150 degrees Fahrenheit can kill most pathogens, viruses, and bacteria. The hot temperature can also soften grime and eliminate greasiness.

  • You can use a thin knife to remove the rubber. However, be careful as this may damage the rubber, making the lid leaky.
  • Let the rubber soak in hot water for five to 10 minutes. 
  • Scrub it using soap, vinegar, or baking soda.
  • Rinse, then air dry. Don't put the rubber back until it's completely dry.


To clean a water bottle's rubber seal, you can scrub it with liquid soap, baking soda paste, vinegar, hydrogen peroxide, and boiling water. Aside from that, take time to remove rust from the bottle and disinfect your bottle so you can use it for a long time.

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