Ninja Coffee Bar Water Reservoir Mold (Cleaning Guide!)

Concerned about possible algae in your Ninja coffee maker’s reservoir? It’s a common misconception. Algae typically form in sun-exposed, stagnant water over time.

In the confined, shaded space of your coffee maker, what you’re more likely to see is mold.

In this guide, I’ll comprehensively address how to clean and prevent mold, ensuring every cup of coffee is as fresh as it should be.

How To Clean Out The Mold In My Ninja Coffee Maker Water Reservoir?

  • Use a toothbrush with vinegar to scrub the screen on the water suction port. For deeper cleaning, remove the screen entirely.
  • Fill the reservoir with a 1:1 mix of water and vinegar, let it sit overnight, then scrub. Alternatively, immerse the entire tank in this solution.
  • Run a 30-minute cleaning cycle for regular mold removal. For severe mold, opt for a 4-hour deep cleaning cycle.
  • To prevent mold, clean the machine every three months and inspect the reservoir regularly. Use filtered water to reduce mineral buildup.

Let’s dive into some more detail on how to do this below!

Mold In Ninja Water Tank

Clean The Water Suction Port Screen

The Ninja coffee bar reservoir has a poor design when it comes to cleaning. There is a small screen on the water suction port that you almost can’t reach under. This means dirt, mold, and hard water deposits often collect there.

Not only can this make your coffee taste bad, but it can also block the water reservoir outlet valve. When this happens, the machine can’t get enough water and will beep five times.

Here is how to unclog the water tank valve:

  1. Remove the water tank from your coffee machine.
  2. Use a toothbrush and some vinegar to scrub three sides of the screen to remove any dirt. One side of it might be tough to clean.
  3. Find the small ‘x’ mark under the tank. Press it a few times using a straw or pencil. After that, blow through the filter to get rid of any remaining dirt.
  4. Put your coffee machine back together.
  5. Refill the tank and try brewing coffee.

Another good way to reach underneath this screen is with a straw brush like this one. These can bend a little making it easier to reach underneath. Just put some vinegar on the brush and start scrubbing.

Take Out The Screen To Clean It More Effectively

If you don’t want one side of the screen to stay dirty, you can take the screen off completely to clean it properly.

Here is how to remove the screen and clean it:

  1. Find the two screws on the screen covered by clear caps.
  2. Carefully remove the caps using a screwdriver or drill.
  3. Unscrew the two screws using a Philips screwdriver.
  4. Take off the screen.
  5. Clean the suction port and the screen with vinegar and water until it’s completely clean.
  6. Place the screen back.
  7. Screw it in place and cover the screws with the caps to prevent rust.

If you’ve drilled and damaged the two caps, you can cover the exposed screws to avoid rust with some glue. Use glue that is both food-grade and water-resistant. This will act like the original caps.

Soaking The Water Tank In Vinegar

If your water reservoir has mold everywhere, not just the valve, you can clean it by filling it with an equal mix of water and vinegar. Leave this mixture in the tank overnight. In the morning, use a sponge or brush to scrub the inside to ensure all mold is removed.

Another option is to prepare a bucket with half water, half vinegar solution and immerse the entire water reservoir in it overnight. This will help clean both the inside and outside of the tank.

Clean Your Ninja From Mold and Mineral Build-Up In The Tubes

If there is mold in your coffee maker’s water tank, it’s probably in the pipes and other parts too. Mold can make your coffee taste odd, like dirt I would say. It’s also unhealthy to drink coffee from a moldy machine.

To remove mold from the tubes and other components inside the machine, run a full descale cycle. If the mold in the water tank seems severe, I recommend the four-hour deep cleaning cycle.

Ninja coffee makers offer two cleaning options: a quick 30-minute cycle or a thorough 4-hour deep clean cycle. You can choose either one.

Here’s an easy guide to cleaning and descaling a Ninja coffee maker:

30-Minute Cleaning Cycle

  1. Empty any water currently sitting in your reservoir.
  2. Fill the reservoir with white vinegar to the “half-carafe” line.
  3. Fill the remainder of the reservoir with water, up to the “clean cycle max fill” line.
  4. Turn the knob to “full carafe”. If you don’t, the machine will start beeping and won’t allow you to proceed.
  5. Press the “clean” button. The machine will begin pulling a bit of the solution into the system, effectively immersing all parts.
  6. Wait for 30 minutes as the machine descales.
  7. Once the 30-minute cycle finishes, all the vinegar-water solution will have been run through and the reservoir should be empty.
  8. Dump out any remaining solution, and rinse out the reservoir.
  9. Fill the reservoir with clean water up to the max fill line, then run the “clean” cycle again. Do this twice.
  10. The “clean” light should then switch off, indicating the cleaning cycle is complete.

4-Hour Deep Cleaning Cycle

  1. Fill the reservoir with white vinegar to the “half-carafe” line.
  2. Fill the remainder of the reservoir with water, up to the “clean cycle max fill” line.
  3. Hold down the “clean” button for 5 seconds to start a 4-hour timer.
  4. The machine will slowly run 9 ounces of the vinegar-water solution through the system every hour, in order to deeply clean the machine.
  5. After the 4-hour cycle, rinse out the reservoir.
  6. Fill the reservoir with clean water up to the max fill line, then run the “clean” cycle again. Do this twice.
  7. The “clean” light should then switch off, indicating the cleaning cycle is complete.

Note: It’s important to distinguish between the “clean cycle max fill” line and the “max fill” line. For these cleaning cycles, always fill to the “clean cycle max fill” line.

Only fill it to the “half-carafe” line when doing the cleaning cycles with fresh water. This will let the machine sense that you’re not trying to brew coffee.

How To Prevent Mold Build-Up In Your Ninja Coffee Maker

Always run a cleaning cycle at least once every three months. However, also check the water reservoir regularly. If you see signs of mold buildup, don’t wait for the three months to pass before descaling again, clean it right away to prevent the mold from worsening.

Try using filtered water. While I doubt this helps against mold buildup, it will definitely reduce the mineral buildup in your machine.

Mineral build-up in your Ninja coffee maker can reduce the amount of coffee it brews and make your coffee cooler. It’s best to keep it clean.


Maintaining the cleanliness of your Ninja coffee maker’s water reservoir is crucial for both taste and health.

While it’s easy to mistake mold for algae, understanding the difference and the conditions they thrive in can guide effective cleaning.

By following the steps outlined in this guide, not only can you tackle existing mold but also prevent its recurrence, ensuring every brew is safe, fresh, and flavorful.

Thanks for reading!