How to Clean a Canister Filter | 17 Step-by-Step Guide

Canister filters should be cleaned every one to three months based on the manufacturer’s instructions, the tank’s water condition, and the type of media used in your filter.  

A canister filter removes all debris and impurities from your aquarium. A filter provides a healthy environment for the survival of your fish and other inhabitants. 

Make sure your filter is operating at its best with routine maintenance. Not cleaning the canister filter routinely can clog it and lead to nitrogen and other chemicals in the water. 

Below is our step-by-step guide with everything you need to know about how to clean your canister filter. 

A Step-By-Step Guide for How to Clean a Canister Filter

We’ve outlined below our step-by-step process for cleaning a canister filter. Starting with the basics of what tools you need for the job and ending with the final step of plugging your filter back in.

Step 1: Schedule

You will need to use aquarium water to clean the canister filter. Because of this, it is best to plan to clean your water filter while you are doing a water change. 

Step 2: Gather the Tools for the Job

• Toothbrush for scrubbing algae
• Scrub pad for scrubbing stubborn algae
• A bucket full of aquarium water
• High-pressure hose, bathtub, or sink
• A bucket full of aquarium water
• Towel
• Q-tip

Step 3: Turn off the Filter

Before touching anything else on your filter, you should turn off the power going to your filter. You can do this by unplugging the filter’s power cable from the power socket. 

To confirm that your filter is off, check the outflow tube. There should be no water coming out of it. 

Step 4: Turn off the Shutoff Valves

Once you’ve unplugged the filter, the next step is to turn the shutoff valves are into the ‘off’ position. This step ensures that water does not spill out when you disconnect the tube from the motor housing.

Step 5: Unscrew the Tubes

Slowly loosen the locking nut from the threaded pipe until it is easy to take off. Water trapped inside the motor housing is likely to leak out. It will not be large volumes, but you should be ready for it. Once the trapped water is out, place the pipes aside.   

Step 6: Move the Filter to a Suitable Location for Cleaning

Next, take your filter to a place where you can comfortably work on it. Keep in mind that dirty water will spill out. 

A bathtub, kitchen sink, or near a hose would be good options. 

No matter where you choose, you will want to make sure you are near a high-pressure water source. 

Step 7: Remove the Motor Housing

To remove the motor housing, you will need to unlock the clamps from all four sides. 

Carefully lift the housing out of the canister. 

Allow any remaining water to fall out of the housing before entirely removing it. 

Be prepared for water to leak out still once you’ve removed the housing. 

Step 8: Remove the Components

Remove everything from the filter except for the trays with the biological media. 

You will want to keep the biological media submerged in the water while cleaning the rest of the filter. 

Submerging the media in water ensures that beneficial bacteria is not lost. 

Step 9: Time to Clean

Take the items you removed from the filter and run them underwater.

Use a scrub pad or toothbrush to remove unwanted algae and buildup. 

Next, give the filter pads a thorough rinsing under a high-pressured faucet or hose. 

The process won’t interfere with the beneficial bacteria in the tank because the housing is what keeps the bacteria.

Step 10: Remove the Impeller

Gently remove the impeller out of the motor housing. Be careful when doing this, as the ceramic part is very fragile. 

Step 11: Clean the Impeller

Cleaning the impeller is crucial because failure to do so can affect the filter’s performance. There is even a potential for it to damage the motor due to the resistance the dirt on the impeller can cause if left unclean.  

Be sure to clean up the plastic sections surrounding the impeller, and that includes the shaft. 

It is best to use a toothbrush to clean it, as using a scrub brush might exert excessive pressure on the impeller and could break it.

Step 12: Clean the Impeller Hole

Take a Q-tip and place it in the hole where the impeller sits. Use the Q-tip to clean out all the grime.

Dirt can accumulate on the sides of the hole, impairing the performance of the filter. You’ll be surprised at the amount of debris collected from this part.

Step 13: Take out the Biological Media Trays

You will want to move quickly on this step to preserve the beneficial bacteria.

Remove the biological media trays and place them in a bucket of aquarium water. 

Now, discard all the water from the canister filter and don’t reuse it.

Step 14: Clean the Canister

Spray high-pressure water onto your canister and rinse it out. You may also use a clean cloth to wipe down the canister sides to ensure you’ve removed any debris and slime.

Step 15: Reassemble

Now it is time to put everything back together. 

Take the filter back to your aquarium and screw the shutoff valves back to the motor housing’s threaded pipe. 

Be sure not to screw them on too tightly as that could damage them. 

Step 16: Turn the Shut off Valves Back On and Refill

Turn your valves from ‘off’ to ‘on.’ 

Due to the presence of (trapped) air inside your canister, it won’t fill back up automatically. 

To fill it up with ease and without making a mess, elevate the locking bracket slightly. The canister will start filling up on its own. 

Keep an eye on the water level and close the locking bracket when the water reaches the motor housing, so no water comes out. 

Step 17: Plug it Back In

Finally, plug the canister in and use the priming button to prime it. Check everything to ensure it is all properly working. 

If there is a problem, you may need to disassemble to make sure everything is connected correctly.  

Common signs that your canister filter needs to be cleaned

Life happens to all of us. We get busy and may miss one of our scheduled filter cleanings. If it has been a while since you have cleaned your filter, here are the top signs that will indicate it is time for a cleaning.  

• The canister filter is clogged
• Debris and other solid dirt are visible
• Your aquarium has high nitrogen levels
• Foul odor from your aquarium
• Cloudy water

Frequently Asked Questions about Canister Filter Cleaning

Final Thoughts

To provide a clean and healthy environment for your aquarium inhabitants, you will need to regularly clean your canister filter. 

We hope our guide has provided enough information about the process and what you need to know to keep your filter operating for years to come. 

Looking for tips about aquarium maintenance? Head over to our Aquarium Maintenance & Repair section to see more.

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