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How to clean a water flosser

How to clean a water flosser


You might not be aware, but mineral deposits from water, mouthwash and other materials can collect on or within a water flosser and may affect the pressure and cleaning effectiveness.

If you want to keep it in great condition and prolong its life, there are a few simple steps that you can take to keep your flosser clean and in good working order.

What are those steps and what is the best way to clean your water flosser?

There is no perfect or must-follow strategy, but the following are common approaches and techniques that manufacturers advise.

If you don’t yet own a water flosser and are doing your research ahead of buying one, you may find our water flosser buyer’s guide useful.

How to clean a water flosser 1

Please note: The following is general guidance that applies most to Waterpik water flossers.  Do always consult the manual for your product to ensure the steps are in accordance with the manufacturer’s advice. Unless specifically necessary, ensure the flosser is disconnected from the power supply before cleaning.


Although you need not do this everyday, it can be beneficial if you complete the following steps once a week.

  • Empty the reservoir and the internal pipework of water
    • The best way to do this is to after use, continue to run the water flosser until there is no more water in the reservoir and none is being ejected from the tip.  Once the water has all gone, continue to allow the unit to run for about 10 seconds, to draw in air though the pipework and push out any residue moisture.
  • Wipe the external surfaces
    • Using a paper towel or damp clean cloth wipe over the exterior plastics, like the handle, hose, main body of the unit and the reservoir to lift any dust, grime or moisture that may have found its way onto these parts.  If necessary use a non abrasive cleaning agent and let it air dry.
    • You may too want to give a wipe in and around the underside of the reservoir as this is a common place for excess moisture to build up.
  • Allow the unit to dry out
    • Lift the reservoir off the unit or position it in such a way that air is more easily able to reach the underside of the water tank and the inlet in which the water flows into the flosser.
    • If your reservoir has a lid, you may want to open this or leave it ajar for air to flow inside.
    • Leave it this way until you next come to use the unit.  The airflow allows for parts to dry out and reduce the chances of bacteria buildup.
How to clean a water flosser 2

Every 4 weeks/month

Following on from the tips above that you should complete ideally once a week the following you should complete approximately every 4 weeks to a month.

Don’t be concerned if you forget or do it every 8 weeks.  The products are well built and designed as best as possible to last.  However, by following these steps you give the best opportunity to your flosser to continue performing at its best for longer.

Clean the water reservoir

The water reservoir or water tank is the part of the water flosser, be that a countertop or cordless unit that you fill up with water and/or mouthwash.

First, ensure the unit is powered off and disconnected from the power supply.

Lift out or disconnect the water reservoir from the unit (refer to your instruction manual if required) to allow you to clean it away from the water flossing unit.

If there is a rubber valve in the base of the reservoir (normally countertop models), remove this and clean it by running it under warm water for 30-45 seconds.  You may choose to use a non abrasive cleaner on it too.

Once the valve is clean, gently dab dry with a kitchen towel and set to one side to fully dry out.

In most instances (refer to your instruction manual), the reservoir can be cleaned, by placing it on the top rack of your dishwasher.  It is advised that you let the reservoir air dry naturally, rather than using the heated drying cycle your dishwasher may offer.

For those without a dishwasher or who desire an alternative option, rinsing with warm water, a soft cloth and a non abrasive soap in a sink is also fine.

Once both the value and reservoir are clean and thoroughly dried, replace the valve by pushing it into place.

If using a Waterpik, ensure that the valve is dome side up, so that when pushed in place the 4 prongs are visible on the bottom of the reservoir.

How to clean a water flosser 3

Clean the internal parts

Minerals and debris can built up within the filters, pump, hose, handle and tip the water travels through.

White vinegar and antibacterial mouthwashes are 2 options you have to flush through the water flosser and clean these internal parts.

Fill the reservoir full of warm water and mix 1-2 ounces (2-4 tablespoons) of white vinegar or mouthwash.

Place the handle of the unit (complete with tip) into the sink and leave the unit switched off.

With the handle and tip facing down into the sink, over a period of about 20 minutes the solution should slowly feed through, draining into the sink and cleaning as it goes.

You can after this time, power the unit on and run through any remaining mixture.

Fill once again with clean, fresh warm water and run a full cycle to empty the reservoir.

The clean is now complete.

How to clean a water flosser 4

Clean the handle and flosser top

For conutertop models you will want to clean the handle.

To do this, press the eject button on the handle to release the cleaning tip.

Place the handle and the flossing tip (seperately) in a container of white vinegar and leave for 5-7 minutes.

Once the time has passed, rinse the handle and tip off thoroughly with warm water.

It is recommended that you replace the tip every 3-6 months, subject to which tip you use (Refer to your instruction manual for more information).

How to clean a water flosser 5

Waterpiks water flossing cleaning advice

As the leading manufacturer of water flossers, Waterpik have put together a video that explains how best to clean their water flossing products.

It essentially demonstrates what I have already mentioned above, but its great to see a physical demonstration of the process.

Your opinions

Do you have any extra tips or advice to give others about how they should clean their Waterpik water flosser?

Do you have a question that has not been answered?

Leave you comments or questions below.

About Jon Love

Jon is a leading voice on electric toothbrushes and has been quoted by mainstream media publications for his opinions and expertise.

Having handled & tested hundreds of products there really is very little he does not know about them.

Passionate about business and helping others, Jon has been involved in various online enterprises since the early 2000s.

After spending 12 years in consumer technology, it was in 2014 that he focused his attention on dental health, having experienced first-hand the challenge of choosing a new toothbrush.

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10 thoughts on “How to clean a water flosser”

  1. I have a handheld Waterpik Waterflosser and at the bottom of the water tank reservoir is a small separate reservoir (at the very bottom) with a pinhole in it. This separate resorvoir cannot be detached from the main reservoir, and it has mold in it. I don’t see any way to clean it or remove the mold. Any suggestions? Thanks.

    • Hi Russell. Do you know what model of water flosser you have? What is this small reservoir for? Sounds like no other way of accessing it.
      Have you tried filling the tank with any cleaning solutions?

    • I have the exact same problem and main reason why I’m searching for how others have cleaned it out. Its a concerning section and really want to figure out a way to clean it so I can continue using the water pik.

  2. I inadvertently discovered that my waterpik was INFESTED WITH BLACK MOLD. I use ACT with fluoride whenever I use my pik, I know that mold/bacteria
    is NOT actually cleaned/removed from the hose portion with vinegar/mouthwash. Could I use hydrogen peroxide to do this?
    I have been sick with a virus probably 5-6 times in THREE MONTHS, could my water pik be the culprit?
    Thank you so much!

    • Hi Julie.

      I can’t say whether your Waterpik would be the culprit of you being sick. Perhaps it is possible, but there are so many variables.

      You should be able to use hydrogen peroxide to clean it if you like.

    • Hi Kenny.

      You mean there is no pressure from the water coming from the tip of the flosser, when you switch it on? It comes out slower more like a tap, rather than the pressure of a water flosser?

      Given it is 3 weeks old, it sounds faulty and you are probably best speaking to the seller for a replacement.

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