How to Clean a Canister Filter (10 simple steps guide with video)

I got a brand new canister filter several months before and I am very happy with its filtration. But then I suddenly realize everything needs maintenance and likely canister filters too. So I reserved some time on a weekend to clean it up.

But it was my first time and I didn’t know how to clean a canister filter? And how often should I clean?

I did some research on the internet and found out people have mixed opinions. Some were saying you should clean after every 6 months (that’s fine) some after 3 months (OK) and some were saying after every month (ok!) and some people were saying you should clean the canister filter after a couple of weeks (now that’s painful!)

I dived a bit deeper and found out that it really depends mainly on how many fishes you have in your tank (stock), what are they and how messy they are.

Some fish are messier than others. For example, goldfish are messier than neon.

So with that out of the way lets move on to the main topic.

How to Clean a Canister Filter (10 step guide)

how to clean a canister filter image

Step 1: Turn off the canister filter

First of all, turn off the canister filter by unplugging it from the socket.

To check if the filter is completely turned off or not, look at the output inside the water tank. There should not be any water coming out from the output tube if it’s completely turned off.

Step 2: Turn off water flow valves

Now shut off the water flow valves of your canister filter.

This mechanism will vary according to the brand.

Shutting off the valves will prevent water from coming out of the tubes when you remove it.

Step 3: Remove the tubing from the input and output of canister filter

First of all, get a bucket or towel around the canister filter. 

It is necessary because when you remove the tubing from the input and output then the water remained in the tubing will come out, so you can put the tubing into the bucket. The water will not be much but sufficient to mess the place.

Now remove the tubing. Again this feature will vary according to the brand.

Usually there will be nuts so gradually lose up the nuts and the tubing will come out.

Step 4. Unlock the motor housing

First of all, make a clear space around your sink and take your canister filter near it.

Now remove the motor housing by unlocking the clamps

The water may come out from the motor housing so hold the motor housing on the top of canister filter until all the water drains out into the canister filter compartment.

Step 5: Remove the components

Before removing the components of the canister liter like media baskets, you should note that you should not remove the water left in the compartment.

Now remove all the components from the canister filter except biological media.

First of all, remove the tray from the canister filter and put it aside.

Now depending on the number of media baskets and the order you have arranged them, remove all the media baskets from the canister filter except the biological media basket.

If you have to remove the biological media basket to remove other media baskets then remove the biological media basket and after removing other media baskets put the biological media basket back again into the canister filter. This is to preserve the beneficial bacteria inside the biological media basket.

You should not remove the biological media basket from the canister filter and put it outside because it will then get exposed to the air that will remove the beneficial bacteria from the water which we don’t want.

Step 6: Wash and rinse media baskets

Now remove the mechanical media and chemical media from the media baskets and rinse the media baskets with water thoroughly.

You may also need to use an old toothbrush to remove the stubborn algae from the media baskets.

Also wash off the filter pads (mechanical media) with tap water.

Now there is a lot of debate on how you should wash the mechanical media of the canister filter.

Some people say that you should wash the mechanical media with the water of your aquarium to prevent removing the beneficial bacteria from it.

But here we are preserving the beneficial bacteria in the biological media basket so there is no point in washing the mechanical media with water from your aquarium.

But if you want to be on a safer side then you can wash the mechanical media with water from your aquarium.

Step 7: Clean the motorhead

Now take out the impeller from the motor housing.

Here you should be very careful about pulling the shaft out because it is very delicate and it can break very easily.

Now clean all the dirt from the impeller with normal tap water.

Cleaning the impeller is very crucial because if you don’t clean it them it can reduce the performance of the motor and potentially damage your motor.

Here you may also have to use a brush to clean the stubborn algae.

Also, clean other plastic parts surrounding the impeller.

Now another important area to clean is the hole where the impeller fits in.

Just as the impeller cleaning, this area is also very crucial because it can reduce the performance of your motor.

You can easily clean this area using a Q-tip or with a paper towel.

Step 8: Cleaning the canister filter compartment

Now here you will have to move fast because now we are going to remove the biological media basket from the canister filter so it will get exposed to the air that may remove the beneficial bacteria from the biological media.

First of all, put the biological media basket out of the canister filter.

And pour away all the dirty water from the canister filter.

Now arrange all the media baskets and the tray in the canister filter compartment and lock the motor housing over it.

Step 9: Reattach tubing to the valves.

Now attach the input and output tubing to the input and output valves of the canister filter. 

Also, don’t forget to shut on the canister filter valves.

Step 10: Priming

Once you have attached the tubing to the valves of the canister filter, plugin and switch on the canister filter.

If your filter is not self-priming then you will have to press the priming button a few times and your canister filter should start working.

How to clean a canister filter (Video)

So this is how you can clean your canister filter. I hope you found this article helpful. If you do then please share it.

Also, let me know if you have any doubts or suggestions in the comments section below.

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