How to Clean Canister Filter? | According to Experts

When I first installed an aquarium at my home, the most important duty was to keep it cleaner and toxicity-free. For this, I attached a canister filter beneath my aquarium. Canister filters are highly effective in carrying out advanced level filtration and feeding effective bacteria to boost the growth of biota in aquariums. However, there are many chances of its fouling due to the metabolic waste of the pets in the aquarium reaching the canister filters. Ten years ago, I asked many professional aquarists and regular aquarium users about how to clean canister filter?

After years of experience in cleaning aquarium filters, I decided to share some practical tricks and tips with new aquarists so that you can keep your fish tank canister filter tidy. By cleaning it, you will be enabling the canister filter to function correctly, and thus your best friends inside the aquarium will be getting cleaner and non-toxic water. So, to read about those considerations regarding canister filter maintenance, all you have to do is scroll down and make notes before you start cleaning your canister filter. Here we go with details on how to clean fish filters!

how to clean canister filter

How to Clean Canister Filter?


A question about how to clean an aquarium filter might be arising in your mind. Suppose you want your aquarium to be super clean and have extra pure water. In that case, you must have installed a canister filter for carrying out the biological, chemical, and mechanical filtration.

If you own a canister filter installed beside your freshwater tank or a saltwater aquarium, there are equal chances of its quality deterioration after use. If you think your canister filter is thronged with the metabolic waste of the aquarium biota, then it’s time to grab a set of tools and clean it.

Required Equipment and Tools

To answer your question about how to clean the canister filter, we must tell you the tools needed. A piece of good news is that all these tools are available at your home or any other commercial store because they are not some special tools aimed at cleaning. To effectively remove the algal species stuck in the canister filter, you will need a toothbrush. In addition, you will see some wastes stuck on the walls of the canister filter, which cannot be removed with the toothbrush.

That is where you will need a scrubbing pad. Also, we suggest you do the cleaning near a sink set up so that you don’t face any issues in walking towards it and using water, slowing down your speed of cleaning. Sinks with the moderate pressure of water will be the best ones to go for. You need to keep with you some other tools: a polishing pad, Q-tip, aquarium water, towel, and cleaner stage for placing your canister filter.

Cleaning Steps

Cleaning the canister filter is not that complicated task as you might be thinking. After preparing the necessary tools for cleaning, the next step is to properly turn off the canister filter by shutting it off from the plug button. Next, you should disconnect it by removing it from the power socket, followed by checking the outlet hose. Make sure that no water flows from your canister filter before you go to the actual cleaning steps. We have outlined some essential steps that you need to follow, and they are:

Entirely Powering Off the Shut-Off Valves

Once you have unplugged your canister filter, you need to power off the shut-off valve in a proper way. Once you do it, you will see no spilling of the water from the canister filter after separating the hoses attached to the motor.

Detaching the Tubes

In this step, you need to unscrew the canister filter tubes and slowly turn the bolt unless and until you see the pipe loosening. By doing so, you will give a chance to the trapped water to release effectively from the housing of the canister’s motor.

Repositioning the Filter

You must find a suitable position to relocate your canister filter to prevent drenching as you clean it. We strongly suggest you place it over the sink with suitable water pressure to help you effectively in easier cleaning. You may also use a hosepipe if you are carrying out the entire process outdoors.

Removing the Motor Housing


You are instructed to loosen the bolts and then release them from all four sides in this step. As a result of this step, you may see some water spilling, but it is all right. You must continue working by removing the canister motor and then placing it on a safe side. For catching extra water spilling, you may use a towel for drying purposes to prevent the floor and sink from flooding.

Removing the other Items and Cleaning


You will see many smaller items present inside your canister filter that might hinder your way of cleaning it properly. Therefore, you need to remove them as well. One precaution you must consider in this regard is not to displace or remove the trays aimed at the holding of the biological media. You need to keep them inside water throughout the cleaning procedure.

By doing so, you will not be causing any harm to the beneficial bacterial strains residing in the tray. After that, you should start washing the other removed items with the toothbrush to remove the dirt. You may use a scrubbing pad for removing the stubborn dirt stuck with the canister filter walls. Also, you can use any type of filter pad where required.

In this cleaning process, you must not forget the removal and cleaning of the impeller embedded inside your canister filter. However, clean it with extra care because it is made with ceramic media, and thus it is prone to breakage. Cleaning the plastic parts is essential, and also you should not exert extra pressure while cleaning the impeller. After cleaning the canister filter, you must watch it closely and check if any debris or dirt has been left from cleaning. If the canister filter is clear enough, you need to wipe it with the cleaning cloth to dry and make it better for use after cleaning.

Reuniting the Detached Assemblage

Once you are done with the cleaning procedure, you need to reassemble the detached components to use your canister filter again to give cleaner water to your tank buddies. In this regard, you need to follow the exact sequence of attachments that you used while removing all steps. However, you need to show some vigilance because the biological media tray you left aside can undergo any damage while cleaning.

Also, we instruct you to be very gentle in tightening the nuts because too much pressure can cause them to become stuck, and you will be in trouble for the next cleaning period. Carelessness in this regard can lead to permanent damage to the piping and other components of the canister filter. After assembling the necessary parts, you can switch the shut-off valves and plug them in to supply clean water for your fish tank.


After how much time should I consider cleaning my Fluval canister filter?

Different brands in the market are manufacturing a wide range of Fluval canister filters. Thus you can understand that they are pretty different in terms of specifications and requirements for maintenance. Therefore, you need to check them before purchasing. For example, if you don’t like frequent cleaning, you can go for Fluval FX6 high performance canister filter. On the other hand, if you are obsessed with your fish’s health in the aquarium, you can go for Fluval 306 External Filter.

Is it reasonable to change the media of the canister filter?

Not at all. You must avoid changing the media in the trays of the canister filter because these trays contain biological organisms in the form of beneficial bacterial strains. These beneficial bacterial strains help your fish biota to grow better. In case of changing the media, you will be losing these bacteria. However, if there are some severe issues with its functionality, then you may change them.

Which media is best for canister filters?

You have the freedom to opt between the ceramic, spongy, and floss media to use in your canister filters. However, if you need media with a longer life span, you must go for the ceramic media that does not require you to change it frequently compared with the spongy media.


After reading this step-by-step guide on cleaning canister filters, you must be in a clear position to start cleaning your canister filters. We hope we have answered your queries regarding how to clean a canister filter and how often to clean a canister filter. We strongly recommend you take extra care in cleaning your canister filters to get the best results.

Also, don’t forget to share your thoughts and experiences regarding the subject matter in the comments section!

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