Cleaning a canister filter ensures that it is running at maximum water flow and filtering at optimum efficiency. Over time the mechanical filtration inside your filter will clog and this is what needs to be cleaned out regularly.

In this cleaning guide I use a Fluval 305 but the principles can be applied to cleaning any canister filter.

1. Things you will need

Here’s a brief list of what you will need to clean out a canister filter:

• old toothbrush
• clear workspace with a sink (the laundry or bathroom are ideal choices)
• a bucket
• a syphon
• an old sock
• a rubber band or some string
• small tub of vaseline


2. Getting the filter to the workspace

If your filter allows for it block off the hoses to maintain water vacuum in the hoses. For the Fluval series of canister filters this is achieved by pulling up the black lever on the hose attachment.

If your filter does not have this capability you might need to withdraw the filter intake from the tank otherwise your intake will draw water upon disconnection from the canister unit.

Once the hose is blocked off or the intake has been removed from the tank it is then safe to turn off power to the canister unit. Once this is done disconnect the hoses (or hose unit if you’re using a Fluval) from the unit and carry the filter to the workspace.


3. Cleaning the mechanical media

Once at the workspace open up the filter (for Fluvals this is lifting the two light grey clamps on either side of the unit) and  have a look inside, it should look gunky like this:


First we will clean the mechanical media as it is easily the most dirty component of a canister filter. With the Fluval models mechanical media is attached to a tray unit. To access the media simply lift the unit as shown below:


Most manuals and fish shops recommend throwing out this media and replacing it with new media, the reason for this is money is made when you are continually buying new media. We don’t throw out kitchen sponges after one use and mechanical media is the same.

It is IMPORTANT to NEVER use TAP WATER to clean canister components as chlorine/chloramine in the tap water will wipe out your biological bacteria and render your filter temporarily useless upon reconnection.

Using your syphon fill a bucket with tank water from the aquarium and use this to rinse off the mechanical media. The bucket water will get dirty fast so use additional tank water as required, I find a bucket of water per 2 sponges is usually sufficient.

Sponges are fairly tough so make sure you clean them thoroughly. You can’t really beat the good ol’ wring it in water till it’s clean technique so I advise to just keep doing this until the sponge is clean.

Below you can see a clean sponge held up against a dirty one. A flash was used the but the dirty sponge is so dirty it still appears black.


Once all mechanical media is cleaned set it aside.


4. Rinse out the biological media (optional)

In the Fluval 05 filters with the stock mechanical media I find the biological filter baskets do get a decent amount of crud in them.

To clean them out I gently rinse them by moving the basket up and down a few times in a bucket of tank water. I use the same bucket of water for all three stacks of baskets. Once rinsed simply set aside the biological media.

If your biological media looks relatively clean and/or you don’t want to disturb it then this step can be skipped.


5. Clean the filter housing

Empty out the gunk water from inside the canister housing and give it a bit of a scrub with your fingers. It is ok for the inside of the housing to feel slimy but remove any solid build up.


6. Cleaning the propeller unit


The propeller unit can be prone to heavy clogging because water flow is at its strongest here. On most canister filters the propeller area can be a bit fiddly to clean so this is where the old toothbrush comes in handy.

If you’re using the bathroom as a workspace make sure you use an old toothbrush and not a current one, that’s a mistake you only make once!

Be especially gentle with the propeller spindle/shaft as they are prone to breaking and are usually relatively expensive to replace for what is essentially a ceramic rod.


7. Put it all back together

Once everything is clean and reassembled it should look something like this:


Nice and clean!

Before attaching the propeller unit be sure to line the rubber seal with a liberal amount of vaseline. This prolongs the life of the seal and stops it from getting brittle over time.

I strongly advise keeping a dedicated small tub of vaseline for this purpose and not just raiding the bathroom cabinet!

After it’s all assembled carry the filter unit back to the tank.


8. Restarting the filter

Before restarting the filter I advise grabbing the old sock (make sure it has been rinsed in normal water and is thoroughly free of detergent or other possible contaminants) and tying it around the filter output as shown on the right.

When the hoses are left for a while without a constant water flow through them gunk starts to fall off the insides and if not caught in an old sock will make your tank look horrible for a few hours upon filter restart.

With the sock over the output it’s now time to prime the filter. For the Fluvals this is simply a matter of clipping the hose unit back onto the top of the filter and then pushing the black lever down. You might have to pump the manual primer a few times to get it going and then water should flow until the canister is full.

For other brands the concept is the same, reconnect the hoses and prime the unit till it is full of water.

Once water stops flowing into the unit it’s time to turn the filter back on. Plug in the unit and watch the outflow, water should start pouring from the sock otherwise you might have to try a few plug/unplugs till it gets going.

One trick I’ve learnt with the Fluvals is that if you pump the primer heavily a few times and plug in the unit whilst doing this it gets it going pretty easily.

Let the flow run for a few minutes and then carefully remove the sock from the output hose being careful not to let the gunk captured escape into the tank.

All done! How easy was that.

Related posts that might interest you:

1. Filtering a Goldfish Tank or Aquarium: Canister Filters
2. Filtering a Goldfish Tank or Aquarium: Internal Filters
3. Choosing a filter for your Goldfish Aquarium or Tank
4. Which filter media to use for your goldfish tank filter?
5. Filtering a Goldfish Tank or Aquarium: HOB Filters