This post may contain affiliate links that support the site at no cost to you. 

If you’re diligent enough to be using a Waterpik or water flosser, it can be pretty upsetting to realize that you’ve got a foul odor going on. 

Like, you are not putting all this time into a multi-step oral care routine to deal with bad smells!

So: if you’ve got a bad smell when using Waterpik, let’s try to narrow it down and figure out where that foul smell is coming from! 

If you’re looking for a full oral care routine, I wrote that too!

Potential causes of bad smell when using waterpik

So, when you’re dealing with a bad odor that appears when you’re using your waterpik or water flosser, it may not be clear if it’s coming from you! 

There are basically two possible sources for the bad smell: your mouth, or the water flosser itself! And both of these are kind of unpleasant to think about. 

We don’t like to think that we might have bad breath! But it’s also pretty gross to think that we might be pumping odor-causing bacteria into our mouth from a water flosser! (And unfortunately, I was traumatized in college by a roommate whose Waterpik tank broke, revealing that it was pretty gross inside.) 

And if you have a bad smell once, don’t freak out! A one-time bad smell is probably just food debris. But persistent unpleasant odor is a sign of a problem.

So, we’re going to use a few steps in this post to troubleshoot your odor issue and figure out where the smell might be coming from. 

Some strategies for keeping your water flosser clean

I prefer to use an inexpensive-but-sturdy water flosser from Amazon and replace it once a year. I’m grossed out by the countertop Waterpiks where the water just sits stagnant for however long it takes you to go through it. If you end up needing to toss your Waterpik, consider replacing it with a travel size. 

I also add a small amount of mouthwash every night to remove bacteria that might be in my tap water! I have heard of people using distilled water to head bacteria off. But I don’t like the idea of all that plastic waste from the bottles, so I don’t do that.

Here’s the inexpensive travel water flosser I use! The cost is low enough that I don’t feel bad replacing it once a year. It’s chargeable, and I probably have to recharge it every four weeks when I use it twice a day. 

(Twice a day might be overkill! But I had some bad breath issues a few years back that got me ON POINT with oral care.)

First: test your water flosser

Okay, so the first possibility that we’re going to test is that the smell is coming from inside your Waterpik. 

(like, “the call is coming from inside the house”!)

Start with a quick visual check. You’re looking for any spots that are black, green, or pinkish orange, or possibly any buildup. 

White residue may or may not be a big deal… If you live in a place with hard water, you can get calcium buildup. That’s harmless and will have no smell. (If you have hard water, you probably also get this residue on your sink or faucet when a water droplet air dries there!)

Honestly, if you find mold, I would just throw it away. If you have one of the really expensive ones and you want to try to clean it, you can use Waterpik’s directions for cleaning your device with vinegar. (But I don’t think I could come back from that, honestly.)

If nothing looks weird, move on to checking the water!

Checking the water:

Now: if your water flosser is currently empty, fill it with lukewarm water. If you’ve got water in there, use what’s in there to see if that’s part of the odor. 

(If you typically add a little mouthwash to the tank like I do, skip that for today.)

Start by checking the smell of the water in the tank. Does it smell normal?

Next, grab a cup, and set the water flosser to spray into the cup. This is a really easy way to test the parts of the water flosser you can’t see. Once you’ve put a fair bit of water in the cup, check to see how it smells. 

If the water smells bad or has any strong odor, you know that your electric flosser is the problem. You can try cleaning it with vinegar if you don’t want to throw it away and get a new one. 

If the water smells fine, try gargling and check for a bad taste. But that’s pretty rare. 

If there’s no bad smell or bad taste, the smell is probably coming from somewhere inside your mouth. Let’s check that next.

Second: test your mouth by quadrant

You might already have a sense of where the smell is coming from, but if you don’t, let’s figure it out. 

You’re going to take your waterpik / water flosser and do 1/4 of your mouth at a time. So, do the top left of your mouth, inside and out, along the gum line. Then stop! Turn the flosser off and just take a second to see if you got that weird taste or smell. 

Then, try the top right of your mouth. Remember to do both the inside and outside of your teeth for each quadrant. 

After a break, then you can do the left and right side of your bottom teeth! 

There are a couple possible results here: you might find that the bad smell appears in all parts of your mouth, or you might find that it’s just in one place, or in a couple spots.

If it’s everywhere in your mouth

 That would indicate that you’re more likely to be having an issue with gum disease, which is one of the most common causes of bad breath. If your breath smells, it is absolutely one of the most stressful and embarrassing things you can deal with.

If the smell is everywhere, the best thing you can do to head off periodontal disease or gum disease (the causes of halitosis) is get a regular dental routine going. Here’s mine, which saved me a few years ago when I struggled with bad breath for months: TKTK. A lot of people will be able to treat their bad breath by themselves by just improving poor oral hygiene. 

(If you’re getting a bad smell off your water flosser and you just started flossing or water flossing regularly, try not to worry yet. The good news is that good oral hygiene can improve or reverse gum disease, so you may well find that the unpleasant smell goes away after you’ve been doing a full oral hygiene routine for a few weeks.)

If your oral health is on point and you’re still dealing with chronic bad breath, there are a few other possible causes. Tonsil stones can cause persistent bad breath no matter how good your dental hygiene is. (Ask a dentist or dental professional next time you’re in the office– they have a distinctive smell that is different from regular bad breath.) Certain types of stomach problems can also be the cause of bad breath. Bad breath can also stem from the back of your tongue, so using a tongue scraper can also help.

If it’s just in one spot or a few spots

If you’re able to narrow it down to one area of your mouth, you might be dealing with tooth decay in that area. Dental problems like decay also have a smell, so bad breath localized to one area can show a underlying issue in that area of the mouth. 

This happened to me while I was pregnant (which wreaks havoc on your teeth!). I kept getting a weird gross taste while I was using my water flosser, just on the top right side of my mouth. When I gargled, it would go away. After about a month of this, a crown fell out of my mouth! I think that when the cement was loosening, the presence of bacteria on the old tooth was leading to decay, and the water flosser water was moving that bacteria (and the taste) around my mouth. 

This was, of course, very gross, but it’s a sign that you need to get in for your regular dental checkups when you have a taste like that! 

Third: follow up with floss 

Okay, okay, I know you got a water flosser because you hate traditional flossing, but grab your floss sticks or traditional dental floss just this once. 

If you had a smell just in one area of your mouth, you’re going to floss on that side, checking the smell of the floss between teeth.

I know this sounds really weird! But it’s going to help you narrow down the issue. 

So, floss between any two teeth — say, the back two molars. Floss really thoroughly in that one spot, then smell the floss and see if you get any odor. 

Rinse the floss or move onto a different section of floss, and do the next space. Check the smell, rinse, repeat. 

This may identify a certain area that has an issue–if so, you should make an appointment with your dentist ASAP. If you don’t find a specific area that you can point your finger at that has an odor, you may have some decay at the gum line or (like me) under previous dental work. It’s still a good idea to get in to see your dental hygienist if you’re sure the odor is localized. 

What to do about bad breath 

Bad breath is so upsetting and can make you so self-conscious. But you can lose the breath mints and stop covering your mouth with a proper oral care routine — I love mine: It improved a little bit right away and a lot over the course of a few weeks, and I feel so much better not worrying about my breath all day anymore! 

Getting used to a longer routine was annoying, but I was super motivated when I was still dealing with the bad breath, and by the time it was resolved, I was in the habit of spending the extra time. In a weird way, I am grateful that I struggled with my breath for a little while, because it set me up with a gum health routine that’s helped my overall health!