How do You Clean a Canister Filter?

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Tank filters come in all shapes and sizes, with most aquarium owners opting for internal filters since they’re easier to maintain and are perfect for beginners. Internal filters are more fitting for smaller tanks that don’t produce enough waste and dirty to justify investing in an external filter.

The latter is ideal for bigger tanks since they provide more power and can support larger environments with more fish. Needless to say, these are the better option for more experienced aquarists or those looking to make the transition towards larger tanks.

If you want to invest in an external canister filter, you need to know how to maintain it properly. The maintenance process is different than that of internal filters because the system itself is different.

Let’s see how the cleaning process consists of.

Cleaning and External Canister Filter

The external canister filter is larger and more complex than internal filters. As a result, the cleaning process will involve several steps that you otherwise wouldn’t cover when dealing with an internal filtering system.

Here are the essential phases to undergo when cleaning your external canister filter:

  • Prepare a bucket with tank water – As you know by now, you should only clean the filtering system with tank water. Never use tap water for that due to the chlorine content or rely on any chemicals to sterilize the filter and kill beneficial bacteria cultures.
  • Disconnect the filter – Cleaning the filtering system involves using a lot of water, and you can’t do that around active sources of electricity. Unplug the filter from all electrical sources before doing anything else.
  • Shut off the valves – Many people will skip this step, causing them to experience water leakage when removing the tubing. Shutting off the valves will prevent that.
  • Unscrew and remove the tubing – Be aware that there will be some water in the motor housing. Unscrew the tubing, empty the water trapped inside and expose the filter media.
  • Remove the motor housing and the filter media – You will need to clean each part separately for more thorough results. Again, you might experience some mild water spillage.
  • Clean the filter media – You can now clean the filter media in the bucket containing the tank water. Rinse carefully to remove all dirt and residues trapped inside and don’t use any chemical in the process. Only rely on the tank water to do the job. If necessary, you can use a toothbrush to remove algae deposits and more stubborn pockets of dirt.
  • Clean the foam/sponge pads – You should also use tank water to clean the sponge that can be quite cloggy in some cases. The dirty sponges will look dark brown in color and will return to a clear golden shade once clean. You can also use tap water for the sponges, so long as you allow them time to dry out properly before reassembling the filter.
  • Clean the motor housing – The motor housing will also contain a variety of cultures of beneficial bacteria, so clean carefully. Only use tank water and remove any visible dirt and algae deposits either with your hand or a toothbrush.
  • Reassemble the filter – You shouldn’t waste time once the cleaning is over since the beneficial bacteria need a wet environment to thrive. If the cleaning is complete, put everything back the way it was, making sure you don’t make the screws too tight. You don’t want to damage them in the process or break something in the filtering system.
  • Turn on the valves – Allow water to fill up the filter as necessary and mount it in its place. Make sure it’s stable and that it’s locked tight, allowing for no loose movements.
  • Plug the filter in – Once everything is in place, you can now plug the filter back and turn it on. Just make sure there is no water spillage near the filter’s electrical source to prevent any unfortunate accidents.

How Often to Clean a Canister Filter?

There isn’t a standard cleaning period to discuss since the answer depends on several variables. Here’s how you should clean your filtering system depending on a number of factors:

  • The ratio of fish to water volume – Many aquarists have large tanks but not enough fish to justify too frequent cleaning. In that case, you should probably clean your canister filter once every 3 months.
  • The type of waterSaltwater filters require more frequent maintenance. This is due to the accumulation of nitrate, algae, and phosphate suffocating the filter and damaging the cultures of beneficial microorganisms. In this case, monthly cleaning should become the norm.
  • Fauna-rich tanks – More cleaning will be necessary if your tank holds many fish. In this case, you should cleanse your filter every time you perform overall tank maintenance, preferably several days after.

As a general rule, filters require more frequent cleaning the more fish you have. You should also note that some fish species will produce a lot more waste than others.

At the same time, your habits will also influence the filter’s effectiveness. If you overfeed the fish constantly or not clean the tank often enough, the water quality will suffer. The agglutinating residues from food leftovers and fish waste will clog the filter fast, decreasing its effectiveness dramatically.

How Long Does it Take to Clean a Filter?

Cleaning an external canister filter may take longer than an internal filter, primarily due to its size and internal complexity. It may also take you longer to clean it at first, while you’re still new at the job. On average, you should spend around 30-45 minutes to clean the filter and all its components thoroughly.

As you get more proficient at it, that time may cut in half, taking you closer to 15-25 minutes.

My advice is not to rush it. It’s better to focus on cleaning the system properly rather than do it fast. After all, you will only perform the cleaning job once every month or even several months.

How Long Can a Canister Filter be Offline?

Many people seem to think that the beneficial bacteria living in the filter cannot live more than 2-3 hours outside their aquatic environment. This is certainly not the case. In case of power outages, your filter should be fine up to 8-12 hours, depending on how much biomass it has.

The beneficial microorganisms can withstand 24 hours or more out of the water in some cases. Don’t worry about it too much, as aerobic bacteria are actually quite adaptable to environmental changes.

Just make sure to place the filter in a darker area to preserve bacterial cultures.

Do You Replace The Filter Media in Canister Filter?

The answer differs since different types of filters require different maintenance approaches. A canister filter coming with multiple sponges should last for quite some time before needing a significant makeover.

The time to change the filter media will vary depending on your tank’s specifics. These include aspects like:

  • How many fish you have – The more fish in the tank, the higher the bioload they produce. The filter will work overtime to cleanse the water of all the impurities and fish waste, leading to the filter media being overworked. In this case, the filter media may need changing every 2-3 months. You only need to change the filter media every 6 months in best-case scenarios.
  • What type of fish you have – Scavengers tend to ruffle up the substrate, sending tons of particles in the tank water. Many of these particles will end up in the filter, further burdening the system.
  • The type of substrate – Sandy substrates are notoriously more taxing for your filtering system due to the smaller particles being sucked in.
  • Overfeeding – If you overfeed your fish, they will poop more often, the excess fish waste putting a lot of stress on your filter.

The pro of having a canister filter is that it comes with several sponges, which you can replace gradually. First things first, sponges will last quite a while since you can clean them gradually to prevent clogging. Make sure you only clean them in tank water to prevent the chlorine in tap water from killing beneficial bacteria.

After the sponges lose some of their structural integrity and effectiveness, I recommend changing them in sequence. Only change one sponge at a time to prevent disturbing the tank’s microfauna.

New sponges will be sterile, and you don’t want that. Replacing just one sponge isn’t disruptive enough to the environment since old sponges contain enough beneficial bacteria to ensure the habitat’s balance.

As general rules:

  • Chemical filter media needs changing after 1-2 months of use
  • Sponge filter media requires changing every 3-6 months
  • Bio-media doesn’t require changing at all


The filtering system is a vital addition to your aquarium, ensuring the environment’s stability and cleanliness. I suggest maintaining the filtering system properly to prevent clogging and ensure maximum efficiency over the years.

If you still have questions on changing, cleaning, or maintaining filters in the long term, check out my other articles on the subject or ask the comment section.

Author Image Fabian
I’m Fabian, aquarium fish breeder and founder of this website. I’ve been keeping fish, since I was a kid. On this blog, I share a lot of information about the aquarium hobby and various fish species that I like. Please leave a comment if you have any question.

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