How Often do You Clean External Canister Filter?

Disclosure: I may earn a commission when you purchase through my affiliate links. As an Amazon Associate I earn from qualifying purchases. – read more

Canister filters currently rank as the most reliable, effective, and complex filtration systems available. The best models can handle hundreds of gallons of water volume and ensure optimal mechanical, biological, and chemical filtration.

They also don’t take up water space since they’re external filters that stay on the outside of the tank.

What’s not to like, right?

Well, the idea is that the filter itself requires cleaning and maintenance to ensure optimal performance in the long run. Generally speaking, there isn’t a set timeframe for when you should clean your filter.

Some people clean it every 30 days, others every 60 days, etc. It all depends on your filter’s size, the tank’s size, the type of fish you have, the fish’s number, how many plants there are, etc.

So, let’s get into the specifics.

How do You Know When to Clean a Canister Filter?

To understand when the filter requires cleaning, you must first know how a fully-functional and optimized piece operates.

The filter should pump a lot of water, and the tank water should get clean and clear soon after plugging the system.

The clearest indicator that your filter is experiencing reduced performance is the lower water volume being moved through the system. Canister filters will eventually get overwhelmed with muck and dirt; it’s just a matter of time.

When that happens, the filter’s power and performance will drop visible, as the filter moves less water and even stops altogether.

You may even detect an unpleasant odor due to the dirty and stale biofilm. At this point, you need to consider general maintenance to get your filter back on track.

How to Clean a Canister Filter Without Killing Bacteria?

The cleaning process is easy and doesn’t require too much effort. Some of the steps to take include:

  • Disconnecting the filter from the power source
  • Separate all the hoses from the canister
  • Open the filter and empty all the residual water accumulated inside
  • Clean (very gentle scrubbing) or replace the filter media if out of service
  • Replace the activated carbon if necessary (no, you cannot reactivate the carbon, as you may have read around the internet)
  • Use a toothbrush or any similar tool to scrub the filter basket(s)
  • Clean the inside of the canister
  • Clean the impeller (disassemble, clean, reassemble)
  • Put everything back, install the new media (or the old, clean one)
  • Mount the filter back into its place and turn it on

As I said, the cleaning process is rather standard. But I didn’t explain how to clean the filter without killing the beneficial bacteria, right? Here’s what to consider in this sense:

  • Keep the scrubbing down – When cleaning the filter media, only remove larger algae, gunk, and muck deposits. Don’t scrub the media clean since you will also remove much of the beneficial bacteria inhabiting the piece.
  • No chemicals – You can use cleaning chemicals like soap or bleach to clean the filter, but not the media. The added chemicals will eradicate the bacteria colonies, sterilize the filter and disrupt your aquarium’s biological balance.
  • Avoid tap water – Don’t use tap water to clean the filter media. Tap water contains copious amounts of chlorine which is toxic to fish. Use tank water in the process and clean your filter media lightly, enough to remove clogging matter but not enough to sterilize the media completely.

But what if you need to replace the filter altogether? The new filter media won’t have any biofilm, right? Right, which is why you should use the old cartridge in combination with the new one for a while.

The bacteria will multiply and migrate to the new media, at which point you can discard the old piece.

How to Make Your Canister Filter Go for Longer Without Cleaning?

A well-maintained canister filter can even go 2-4 months without cleaning, while an improperly maintained one may require monthly maintenance.

Why the difference? There are several strategies to consider that are meant to lower the maintenance frequency:

  • Relocate the intake – The filter’s intake sucks in the water to carry it through the filter’s internal mechanisms. If the intake is too close to the substrate, it will suck in a lot of matter like sand, dirt, rocks, plant matter, etc. All these will clog the filter fast. Keep the intake at a safe distance from the substrate, preferably around the middle area of the tank.
  • Don’t overfeed the fish – Overfeeding causes multiple issues, but you’re mainly interested in 2: excess fish waste and excess food residues. Both of these force the filter to work overtime and raise the need for more frequent filter maintenance. Only provide the fish with 1-2-minute meals and try to vacuum any food leftovers on the spot. If you have a sandy substrate, the vacuuming process shouldn’t last more than a minute or 2.
  • Consider the fish species – Some fish are messier than others. African cichlids and goldfish, for instance, produce more waste than other species. Goldfish are notorious in this department. Settle for angelfish, bettas, diamond tetras, or discus fish, among others. These produce less poop and aren’t as messy eaters as the previous ones we’ve mentioned.
  • Consider 2 filters – This is common practice in large aquariums with a lot of plants and fish. One filter-only may not provide sufficient power to support the entire system. Sure, there are canister filters that can handle 200-400-gallon setups, but there’s a tradeoff to consider. The filter needs to operate at a higher power to ensure optimal results. And many fish and plants hate water currents. A 2-filter system circumvents the problem, providing calm and clean waters and retaining their peak operating conditions for longer.

As you can see, you have ways to lower the need for frequent filter maintenance. I recommend embracing several for the best results.


Canister filters are great additions to any aquatic setup, but they require regular maintenance themselves to operate at their peak. Fortunately, canister filters are the easiest to clean without disturbing the environment.

And they last the longest without cleaning, provided you follow my tips in this sense.

So, follow them!

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.
Leave a Comment

Your email address will not be published. Required fields are marked *