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How to clean a water flosser

How to clean a water flosser - header image


So, you have your water flosser, be that market leader Waterpik or from another brand.

You might not be aware, but mineral deposits from water, mouthwash and other materials can collect on or within your 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 for cleaning your water flosser, 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 manufacturers 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.

How to Clean a Waterpik® Water Flosser

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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6 thoughts on “How to clean a water flosser”

  1. Hi, I have the WF A10 model . Love it!! My water reservoir has a cone shaped bottom with a tiny whole in which water can seep through to the small chamber below. This chamber needs cleaning but I can’t access it and am afraid to force it in case I break it. Don’t have my instructions and cannot find this particular info on line. Please help!
    Regards, Marian

    • Hi Marian. I don’t think I am familiar with the A10 model. Is this made by Waterpik? Perhaps it goes by another name I might know. Apologies if I am missing something obvious!
      Have you tried contacting the manufacturer for advice?

  2. Hi Jon. I have a countertop water flosser which recently produced this disgusting algae-like slime out of the handle, I think because the handle had split slightly and it was able to suck air into the handle and therefore force the slime out (no head was attached at the time). I assume the slime had built up in the handle/cord. I have been very reluctant to use my flosser since then. Is there any way to ensure no similar build up will occur?

    • Hi Laura. I have not experienced this before. The split handle that you think caused it has now been fixed/replaced? I can only suggest regular cleaning of the flosser and all being well things should be fine.

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