How to clean your cat’s water fountain pump

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The first time we noticed our cat’s water fountain stop running, we assumed the pump had broken down. After all, it was just a cheap water fountain, not a fancy branded one, and probably came with poor quality parts. No big deal; we ordered a new pump.

While the new pump was on the way, my partner James – ever the engineer – decided to take apart the pump “just for fun”. Surprise, surprise: despite cleaning the fountain and replacing the water filters regularly, the inside of the pump was filled with gunk and slimy pink residue – which isn’t mould by the way, but an overgrowth of the damp-loving Serratia marcescens bacterium.

After giving the pump a thorough cleaning, we tried running it again – and it was good as (m)ew!

Why should you deep-clean the water fountain pump?

If you’ve had issues with the water flow from your pet fountain, the pump could well be clogged up inside. In fact, you might have been like us – cleaning the fountain religiously only to find pink slime proliferating. We’d thought this was because we live in a hot and humid climate or because we feed our cat raw food, but since cleaning the pump regularly, we’ve had way less issues with slime and can replace the water filters less frequently.

Deep-cleaning the pump not only saves you money from replacing the pump or your entire fountain, but also ensures that your entire fountain system is kept clean. If your cat has been refusing to drink from its water fountain even after you’ve cleaned it and filled it with fresh water, try checking the pump. (Or, your cat might just be bored!)

Steps to clean a pet water fountain pump

Most pet water fountains come equipped with the same sort of small submersible pump. Yours may vary slightly in appearance, but the inner parts should be the same. If you’re unable to find or remove any of the parts in the steps below, do not force anything open.

We take no responsibility for any damage resulting from incorrect attempts to dismantle your pet fountain pump.

1. Remove the pump from the pet fountain

Most pet fountains have a removable submersible pump to keep water flowing. The pump is usually kept in place with suction cups. If your pet fountain has a different system, this guide won’t work for you.

2. Remove the front and back cover

A pet fountain pump with front cover removed, showing the dirt and gunk inside.

This might take a bit of tugging, but don’t worry – they’ll snap right back on when you’re done. After removing the front cover, you’ll likely see another round piece covering the pump rotor. Remove this too.

3. Pull out the pump’s rotor impeller

A pet fountain pump with inner cover removed, showing the rotor.

You may need a pair of tweezers to get a grip on this part, but it should slide out easily. Look at all the gunk that’s built up inside!

4. Scrub and rinse all the pump parts

Pet fountain pump with cover and rotor impeller removed for cleaning.

Use dish soap and a toothbrush or pipe cleaner to get at all the pump’s nooks and crannies. Don’t forget to also clean the power cable where it meets the pump – that spot is often overlooked. Once you’re done, rinse and reassemble the pump.

5. (Optional) Run the pump in soapy water

Time to suds it up! Add dish soap to your pet water fountain or another container and let the pump run. This gives the inside of the pump a good clean as well. Then, rinse everything thoroughly and run the pump again in clean water to ensure there’s no soap left.

6. You’re done!

Stainless steel Pioneer Pet fountain with adjustable flow pump

Stick the pump back in your cat’s clean water fountain and refill it. Replace the water filter (if there is one). Now your cat can enjoy fresh water again.


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