How to Remove Mold from the Rubber Seal on a Water Bottle

When you see black dots before your eyes, that could be a bad sign!

Maybe you’ve just seen spots of mold in the rubber seal of your water bottle. Mold may multiply and grow, like the spots on snow spread by the Cat in the Hat. And isn’t mold supposed to be bad for you?

Before you toss that water bottle into the garbage – there’s a way to revive that bottle and boost your zero waste footprint in the process.

There are several proven ways to clean mold from a water bottle - allowing you to know the water in your bottle is safe to drink. I'm going to share a specialized cleaning method, for plastic or stainless steel water bottles, that's worked great at home for me, my family, and friends.

Understanding how mold grows and how to prevent it

When you drink from the water bottle, your normal salivary bacteria enter the bottle. Any invisible spores of mold may develop from those bacteria, and they’ll thrive in warmth, moisture, and light.

Even bacteria left behind when you thought you’d washed the bottle out properly the day before, may start the growth of mold, which may take a day to two to become visible. 

A regular wash of your bottle with hot water and dish soap may not be enough to clean out any residue of bacteria, so eliminating mold requires a specialized cleaning process.

First things first - when you see mold around the neck of the water bottle where the lid seals, stop drinking that water immediately!

Now read on to find out how to refresh your water bottle.

What you need to clean mold from your water bottle seal:

  • Rubber gloves
  • Water
  • Liquid dish soap
  • Vinegar (one part vinegar to one part of water) OR
  • Bleach (sodium hypochlorite) (one part bleach to four parts of water)
  • A bucket or sink
  • A soft cloth or a hairdryer
  • A drying rack

Cleaning mold from water bottle seals


Start with your regular wash of the bottle in hot water and dish soap, but use a soft bottle brush to clean out all the inner folds and outer surfaces of the seal.  Then immerse the cleaned bottle and lid in a mixture of water and white vinegar (equal quantities of each) and leave to soak (overnight).  White vinegar kills 82% of mold spores. Alternatively, soak the bottle and lid in a bleach solution (one-part bleach to four-parts water). This kills more bacteria.


Now that the vinegar (or bleach) has killed the mold, the seal should be scrubbed clean. Use 2 teaspoons of baking soda mixed to a paste with a little water, and rub it into all the creases of the seal, leaving it to work for 10 minutes.


Wash the bottle and the lid, thoroughly (as in the first step) again, paying special attention to the seal. Rinse thoroughly with clean water.


Dry the bottle and lid, with a soft cloth, focusing on drying out all the creases in the seal -   (you could even blast it with a hot hairdryer) – and set it out to dry on a drying rack.


When it is completely dry, you may use the bottle again, by filling it with clean water and closing it properly with the clean lid.

Growing a new habit

Try to get into a flow with this - clean it every time you've used the water bottle.

Pro-tip for sustainably clean water bottles

The dry-out at the end is very important, so use the hairdryer on HOT to heat and dry the bottle, its seal, and the lid.

Top 5 Sustainable Water Bottles

Time for a new water bottle? I tried dozens to narrow down my 5 favorites.


Why do water bottles get moldy?

Bacteria are introduced from your mouth when you drink from the bottle; you may not have cleaned the bottle well enough before using it; bacteria grows once the bottle is opened, and eliminating mold requires a specialized cleaning process.

How do you clean your water bottle to get rid of mold on the seal?

The short version - wash it well in hot soapy water, scrub with a soft bottle brush. Then soak it in either a vinegar or bleach solution overnight. Then rinse and dry thoroughly. And always seal the bottle tightly when you fill it with fresh water.

Can black mold on a water bottle make you sick?

Yes, mold is seriously harmful – different from mildew – and can cause nausea, diarrhea, vomiting, respiratory problems, and bleeding from the nose and mouth.

Does vinegar damage silicone?

No, vinegar does not damage silicone but may damage products that have a structured membrane or varnish, like tiles, or pearls.

Final thoughts

I hope you found this lesson in cleaning your water bottle seal useful - if so you might also like my guide for cleaning spray bottles and stainless steel water bottles. The aim of a zero waste lifestyle is to avoid throwing away items unnecessarily – you’re doing something to cut down on pollution and waste.

Plus, it's always great knowing the items you and your family use every day are clean, germ-free, and good to go.

Now get out there and drink in the glow of the day.


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