Black Stuff In Your WaterPik Flosser – What Is It And Is It Harmful?

WaterPik flosser is a recommended alternative to anyone who has troubles with traditional dental flossing. It involves the use of lukewarm water to spray the teeth and remove food particles hanging around. As it is meant for oral health, it can be a bit shocking to find black stuff in your WaterPik Water flosser.

Black stuff in your WaterPik flosser is mold, which can be eliminated using a white vinegar and warm water solution. Mold can live and grow anywhere with high humidity or moisture, which makes your Water flosser an easy target.

In this article, we will cover the reasons why there is black stuff in your WaterPik flosser, how to remove the black stuff, and how to prevent mold growth in your flosser. We will also explain how to clean the different parts of your WaterPik flosser and how to fix low-pressure issues in your flosser. 


What is a WaterPik water flosser

A water flosser is a device that is designed for oral health and dental care. It usually has a motor with pump, a special flosser tip, and water reservoir, and it comes in different sizes and styles. Your WaterPik water flosser is no different. 

The motor with pump provides pressurized and pulsating water through the special tip into the mouth. The spray of water removes food particles, plaque, and bacteria effectively and comfortably compared to traditional flossing with string. The action of the water also stimulates gum tissue for added health benefits. This flosser reaches places in the mouth that most regular flossers will not get to.

You can use a WaterPik flosser if you feel uncomfortable with string floss. It is also useful for cleaning difficult to reach places such as braces, dental implants, crowns, and other orthodontics. If you’re dealing with inflammation of the gum around some parts or all of the teeth, then a WaterPik flosser can be a great flossing option.

Your WaterPik flosser is of course frequently in contact with water, which makes it the perfect place for mold to grow if you don’t take care of it properly.

What is the black stuff in my WaterPik?

Mold is a fungus that can begin to grow on WaterPik water flosser tips and on the edges of the water chamber. Black mold produces mycotoxins that can cause skin irritations, allergies, and fungal infections in humans and should be immediately removed and the flosser system sanitized.

Mold will grow anywhere with moisture, usually in the dark and at room temperature.

As your WaterPik is regularly in contact with water, and you probably keep it in your warm and wet bathroom, it’s likely you it will develop a mold growth at some point if you don’t clean it regularly. This is especially true if you leave residual water in your flosser reservoir and don’t wipe it down after use.

Mold requires oxygen to grow, so you wont’ find mold growing underwater in the water chamber. This means that while you could get some mold growth on the flossing tip or in the water reservoir you won’t get mold growing IN the water.

To avoid mold growth, it’s important to regularly change the water and clean the water chamber and flosser tip. Here’s a summary of how you should clean and remove the black mold from your WaterPik:

How to remove mold (black stuff) in your WaterPik

To properly clean mold from your WaterPik flosser, you need water, soft clean cloth, mild liquid soap, vinegar, and/or a dishwasher.

For the best results, clean the outside of the unit, the water reservoir, the internal parts, the handle (for countertop models), and the flosser tip at regular intervals.

Clean the exterior of your WaterPik flosser unit by wiping it down with a soft cloth and a mild non-abrasive cleaning solution. While doing this, make sure that the motor and the base of the electrical cord do not come in contact with water.

Allow the unit to air dry before the next use.

You can clean the handle in the countertop WaterPik model by detaching it from the unit, soaking in a cup with a mixture of warm water and white vinegar in equal quantities, and then rinsing under warm water.

To clean your WaterPik water reservoir:

  1. Detach the water reservoir from the unit. Check the dismantling procedure in the section below.
  2. If you own a countertop model that contains a small black reservoir valve at one side of the bottom, remove the valve by pressing on it. Massage the valve under warm water for 30-45 seconds and then set it aside.
  3. Place the reservoir in the top rack of your dishwasher. It is advisable to air dry your reservoir rather than use the heated cycle of the dishwasher.
  4. If you removed a valve, place it back with the dome side facing up in the reservoir before use.
  5. You can also hand wash the reservoir with warm soapy water, and air dry.

To clean the WaterPik flosser tip: 

  1. Use the eject button to remove the tip from the flosser unit
  2. Soak the tip in a mixture of water and 3% hydrogen peroxide or vinegar, with water being twice as much as the other solution (2:1 water to vinegar / hydrogen peroxide). Do this for five to seven minutes.
  3. Take out the tip, rinse under warm water and it’s ready for use.

To remove mold from your WaterPik reservoir, you can also try using a higher concentration of white vinegar solution (equal volume of water and vinegar) and let it sit for about 20 minutes. This soaking period will also allow the vinegar to dissolve any deposits in your waterpik flosser and clear out all biofilm (bacterial buildup) and mold.

You can also run the vinegar solution through the flosser, the vinegar will be able to clear out residual particles in the hose of your flosser.

How to prevent mold growth in your WaterPik flosser

The easiest way to prevent mold growth in your WaterPik water flosser is to ensure that you use your flosser regularly. This consistency gives you the opportunity to rinse the tip and the internal parts on a regular basis, even if it’s with plain warm water.

If for any reason you haven’t used your WaterPik flosser in a while, make sure to clean the internal parts and the tip especially, before use. 

You can also prevent mold growth in your WaterPik flosser by making sure you completely empty the reservoir after every use. Still water in the device is one of the main causes of mold growth.

Regular maintenance like periodic cleaning of different parts of the unit will not only prevent mold growth in your WaterPik flosser, but also prevent mineral deposits, which prolongs the life of the flosser.

How often can you clean your WaterPik flosser?

A WaterPik flosser has two main parts: the tip and the water reservoir. For the water flosser tip, replace it every three to six months to prevent unhealthy mineral deposits or mold from building up. 

For the water reservoir in the water flosser, clean it every one to three months to maintain the best performance. If you live in a warmer climate, you may need to do this more frequently to prevent the buildup of any biofilm or mold in the reservoir.

How to disassemble a WaterPik flosser for cleaning

Disassembling is important to perform routine cleaning on your water flosser, and since the WaterPik flosser is a simple device, it’s very easy to take it apart for maintenance purposes.

The process differs slightly between model, so for more tailored instructions, refer to the products manual page on the WaterPik website and select the one specific to your model.

  • The first thing to do when you want to disassemble a WaterPik flosser is make sure that the unit is turned off.
  • To remove the water flosser tip from the handle, there’s an eject button on the handle that you can easily slide down. 
  • To remove the reservoir, slide it down to the base of the unit for handheld models, or pull it up from the base of the unit for countertop models. 
  • Some water flossers have a reservoir valve at the bottom. You can detach that by pushing it up from the bottom of the reservoir before taking care of the reservoir.

Other parts of the reservoir do not need to be disassembled for maintenance.

Why is your WaterPik Water flosser losing pressure?

The pressure of a WaterPik water flosser is helpful to flush away any particle build-up in hidden corners of your teeth and gum. The pressure settings on a WaterPik flosser differs by model and size of the flosser. With pressure settings ranging from three to ten levels, and a working pressure ranging from 10-90 PSI, the pressure output will be different.

So when your WaterPik flosser starts losing pressure, it is possible that:

  • There is a collection of mineral deposits, mold, and other materials in the WaterPik flosser which is hindering the water flow
  • The pressure settings may be reduced to a very low level
  • You are used to running the battery down completely before recharging
  • The type and quality of the battery used in the cordless flosser is of low capacity, and causing low performance. Or the battery has lasted over 40 runs, which is the typical battery life.
  • You have put the flosser in storage for a long time without prior charging

One or a few of these conditions can cause any water flosser to noticeably lose pressure.

How to fix your WaterPik flosser when it’s losing pressure

There are three ways to fix your WaterPik flosser when you notice that it’s losing pressure. You can either do one of them, and test the resulting effect on the flosser pressure. Or you can combine all three solutions.

  1. Clean your water flosser jet tips
  2. Recharge the cordless models for about 3-4 hours or replace the batteries (for battery models). Two important things to keep in mind when changing the batteries: change all the batteries in the WaterPik flosser at the same time and use Alkaline or NiMH AA batteries.
  3. Clean the internal parts of your WaterPik flosser reservoir. There are two slightly different approaches for the countertop models and the cordless WaterPik flosser.

To clean the Countertop models:

  1. Turn off the unit completely.
  2. Get 16 ounces of warm water and mix with 2-4 tablespoons of white vinegar.
  3. Fill the reservoir with the cleaning solution
  4. Run half of the solution through the Water Flosser.
  5. Place the Water Flosser handle in your sink and allow the solution to gradually drain out through the handle.
  6. Run any remaining solution through the unit, fill the reservoir with warm water and then rinse.

To clean the Cordless models:

  1. Add 1 tablespoon of white vinegar to a reservoir filled with warm water.
  2. Point the handle and water flosser tip into the sink.
  3. Turn the unit ON and run until the reservoir is empty.
  4. Rinse by repeating the process with your water flosser reservoir full of clean warm water.

Other maintenance tips for your WaterPik flosser

The WaterPik flosser is a useful addition to your dental health care kit. The longevity of this device depends on the state of the water you run through it – hard or soft, your cleaning routine, and overall maintenance practices. The effectiveness is expected to reduce if mineral deposits from your water source accumulate in the reservoir or the valve over time. However, there are some simple things you can do to prolong the life of your WaterPik flosser.

These include:

  • Do not immerse the WaterPik flosser unit in water. If there’s any need to clean the entire unit, follow the steps above to disassemble the unit and clean accordingly. 
  • Turn off the unit after use and unplug from the light source, if applicable. 
  • Empty all liquid left in the reservoir after use, even if it’s just water. Remember, mold thrives in moist environments, and you don’t want that anywhere near or in your flosser.
  • After using any special solution like mouthwash, rinse the unit with warm or ordinary water before emptying and keeping for future use. 
  • If you’re using a cordless model, when you replace the battery, apply a very thin and even film of petroleum jelly to the battery cap and compartment sealing surface of the flosser. This will help with a firm water-tight seal.
  • Most importantly, stick to the cleaning and replacement routine for your reservoir and flosser tip.


WaterPik is very effective in managing gingivitis and some other dental health issues. It should not be a source of other health complications to you. 

The cleaning steps for removing mold in the WaterPik reservoir and flosser tip are simple enough to follow. Keep an eye on your flosser for any new black mold buildup and be faithful with your cleaning routine routine. Prevention, they say, is better than cure.

Theresa Orr

Theresa Orr is an Earth Scientist who specializes in determining past climates from rocks using geochemistry. Her passion for clean water drives her to breakdown the science to provide easy to understand information that everyone can read.

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