How To Clean A Canister Filter

What to Know When It's Time To
Clean Those Cans!

Canister filters are a heavily relied upon means of mechanical, biological and chemical filtration in many freshwater aquaria. They extract particulate matter and waste from the water column by filtering the water through sponges (mechanical),  filter media (biological) & water treatment products such as Purigen (chemical). However without proper maintenance, canister filters can quickly become what is referred to as “nitrate factories” as the waste which they removed from the water begins to break down and return unwanted nutrients back into the water column. In order to avoid having your canister filter work against you and your water chemistry, it is recommended that you clean your filter at least every 2 -3 months depending on your aquarium stocking level.
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Before you start dismantling that can, here is a how-to guide with some helpful tips! We will be modeling this process on one of our Fluval FX6 canister filters which we have running on our 150 gallon discus tank. However, the procedure and recommendations can be transferred to any canister filter cleaning.

1. Timing - We recommend planning to conduct your canister filter cleaning on the same day as  a water change. After your filter change is complete, it will probably spit a bit of loose debris into your aquarium which you will then want to siphon out. Additionally, during the filter cleaning itself you will need to rinse off various filtration pieces within the canister. It is recommended that you use aquarium water for rinsing instead of water straight from your tap. This prevents killing off large quantities of beneficial bacteria you have living within your filter.
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2. Location - Consider where you are going to clean your filter. This can be a wet and messy venture so select a suitable location accordingly. Due to the size of the Fluval FX6 we choose to clean the canister outside and utilize plastic tubs for this endeavor. However, if the great outdoors isn’t for you, consider conducting cleanings within showers or bathtubs.
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​3. Let's Get Started - You will need to unplug your canister filter. Next you will need to detach your intake and outflow tubing from the canister itself. Many canister models will have a design feature  which enables you to use a valve in order to cut off water flow through the tubing lines. If your brand of canister does not include this feature, you will need to remove the intake and outflow spigots from the aquarium BEFORE removing them from your canister. The tubing lines will create a suction within your aquarium and begin siphoning out water straight from the tank and onto your floor!

We've labeled our intake and outflow tubing for easy identification.

4. Drain Away - Begin removing the water from the canister. Do not dispose of the water, KEEP IT! Even though it may look yucky, you will be using this water to aid in cleaning steps later in the process (remember it is to save that precious bacteria you spent all that time developing while cycling your tank). Simply empty the water directly into a plastic container or into a closed tube. Many smaller canisters can be physically lifted and overturned to drain water. The Fluval FX6 model comes with a convenient drainage hose and valve located at the bottom of the canister to allow easy means of water removal.

When draining canister water, make sure to save it! You will need it for cleaning.

​5. Watch the Clock - Once the water has been removed from the canister, beneficial bacteria housed within your biological filter media will begin to die. Don’t fret! You still have lots of beneficial bacteria residing within the tank itself and not all of the bacteria housed within your canister will die. Placing biological filter media within the salvaged water removed from the canister will aid in keeping bacteria alive. However, when conducting this process, the longer you take the more bacteria you will potentially lose. So don’t doddle through the next steps of this process.
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6. Cleaning Mechanical Filtration - Sponges and filter pads can become rather grimy and coated in debris and fish waste. You will need to rinse off theses items using the saved canister aquarium water. If you need additional water, you can always remove some more from your aquarium. Simply rinse off the sponges and filter pads to remove any collected gunk. Do not attempt to over clean your mechanical filtration! These items also house beneficial bacteria and we wish to keep as many alive as possible. The primary focus of cleaning mechanical filtration is to clear them of any noticeable debris which might cause clogs within the canister.

7. Biological Filtration - Filter media should not be overly tampered with during this process. Visually inspect the media to determine if any build up in waste or debris is present. If so simply rinse the media with aquarium water to remove the accumulation. We generally rinse our filter media with aquarium water during every filter cleaning.

All filter media is being rinsed with water draining directly from the aquarium.

​8. Exchanging Chemical Filtration - There are numerous options on the market in regards to chemical filtration to help you obtain the water chemistry you desire. Filter cleanings provide the opportunity to reach these chemicals for exchange. On our discus tank we utilize Seachem’s Purigen & PhosGuard. Purigen is an organic waste removal product which we utilize to help keep ammonia, nitrite and nitrate levels in check. It is easy to identify when the product is exhausted due to a noticeable color change. PhosGuard is utilized to help control phosphate and silicate levels in an effort to minimize unwanted algae build up.

Seachem Purigen

9. Inspect the Canister - Once your media has been cleaned, rinse the canister itself to remove any unwanted waste or gunk which could accumulate on the sides of the inner chamber. This is also a good opportunity to inspect the filter components such as the motor or O-rings to determine if additional components need to be cleaned or replaced. We typically dismantle the motor on our FX6 every 6 months to keep it clear of obstructions which could stress the motor.

Dismantling the pump for cleanings to prevent blockages.

​10. Time to Wrap it Up - After you have cleaned and inspected all you media and filter housing, it is time to repackage everything within your canister. Before closing the lid, you might want to add consider adding some water from the aquarium back into the canister. If your canister included the design feature of cut off valves on your tubing, this this step won’t be necessary. Once you have reattached the tubing and opened the valves, water from the tank will begin to siphon back into your canister. After you are certain that water once again resides within the canister it is time to plug in the canister once again.

11. Priming - Many filters have design components to aid in priming the unit in order to restore normal filter operation. Some include push pumps or special techniques. You will need to consult your operation manual for priming features specific for your unit. One great benefit of the Fluval FX6 is that it self primes. After plugging in the canister it will run for a few minutes then shut off. This enables the unit to prime itself and will begin normal operation within a few minutes of powering off. Keep in mind that once your canister is working again, depending on your model it could take anywhere from a few hours to a few days for bubbles to diminish from the system.

Adding water back into the canister through the intake tube.

​12. Just When You Thought Your Work Was Done - Once the filter is running once again, it is fairly common to witness excess debris being kicked back into the aquarium. This is the perfect opportunity to conduct a water change on the aquarium, make sure to siphon out as much particulate matter as possible.

Be prepared for some debris to be kicked back into your tank following a filter clean!

After cleaning your filter and conducting your water change, you might want to consider dousing your tank with some beneficial bacteria to encourage their re-population within your canister filter. We typically add Seachem Stability following filter cleanings.

While cleaning the canister filters on aquariums is one of the more mundane roles of being an aquarists, it is absolutely necessary to stay on top of it. Remember if you push back filter cleans, all the waste it removed from the water column is still accumulating within the chamber. Don’t let it become an out of sight, out of mind situation! If you ignore filter changes, nitrate and algae issues await you in the future. After all, who doesn’t mind getting a little wet & dirty for our aquatic friends!?!

Well that’s all for this time. Keep Krill’in!