How To Clean Your Aquarium’s Canister Filter

If you have just bought a nice, shiny new canister filter for your aquarium, you might want to know how to clean it.

It is inevitable after all.

Or perhaps you have had a canister filter for a while now, and it is becoming necessary to clean it.

Regardless of why you are here, it is clear that you need to know how to clean one of these filters. 

Luckily for you, we have an article here that will guide you through what you will need, as well as give you easy steps that will clearly tell you the process.

So, without further ado, let us begin. 

What will you Need?

The first thing you will need to know is what tools and chemicals you will require in order to clean a canister filter.

So, if you want to get your hands dirty and clean this piece of equipment, this is what you will need to get started: 

• Towel
• Q-Tip
• Scrub Pad
• Tooth Brush
• Sink or Hose
• Bucket of Aquarium Water
• Workspace

Let Us Begin

Hopefully, you have acquired everything on the list, if you have not, you can go gather it all, and we shall begin. 

Okay, we trust that you have everything, and we can begin telling you the steps you will need to take in order to clean your canister filter. 

The method we are about to show you can work for many models of filter, but it may now work for all of them.

In cases where this guide does not work, it is best to check with the manufacturer’s instructions. 

With all of that out of the way, let us begin. 

Step 1- Turn Off the Filter

As obvious as this is, it is a very necessary step.

So, you will want to turn off the filter, unplug it from the plug socket and make sure that there is no water coming out of the outflow tube before you carry on to step two. 

Step 2- Turn Off and Shut Off the Valves

Once you have unplugged the canister filter, make sure that no water is coming out of the tube.

Your next step should be to turn the shut-off valves into the off position, this is so that water cannot spill out while you are disconnecting the filter from the tubes and motor housing. 

Step 3- Disconnect the Tubes

You will need to turn the locking nut off of the threaded pipe until it is disconnected.

At this point, you can expect some water that was trapped in the tubes to come out, so make sure that you are prepared for that.

But, it should not be too much water that comes out.

Once the pipes have been disconnected, you can set them aside.

Step 4- Turn Move the Filter

The next thing you will need to do is move the filter, you will need to do this so that you do not get everything wet with the next steps.

So, make sure that you do the next steps outside, or in the kitchen sink.

Some people prefer to use the sink so that they do not have to move everything too far away from where it goes. 

Step 5- Take off the Motor Housing 

In order to remove the motor housing, you will have to release the lock at each side of the housing.

Do not be alarmed if some water comes out, luckily you are now doing this step in a sink or outside.

If you are doing this step on a counter, you can place a towel under the filter so that when you remove the housing there is not so much to clean up.

Before you move on, it will be important to drain the housing so that there are no unexpected spills on the counter or table you are working on. 

Step 6- Take out the Insides

Once the locks on the sides of the housing have been removed, you can remove the housing.

Make sure to do this gently so that nothing inside is damaged.

Set aside the shell, and you will have all the motors revealed.

You may get a bit more water spillage, but if you are doing this over a sink or with a towel under you, there should not be too much mess. 

With the motor house off, you will need to remove everything within the filter.

Leave only the trays that hole the biological media.

Make sure that these trays remain submerged in water while you clean the other filter components.

This will prevent you from losing the beneficial bacteria that your fish need to survive.

While you are doing all of this, you will need to keep everything quite close together so that you can put them together quickly once you are done cleaning. 

Step 7- Begin Cleaning

You will need to use a sink or hose for this step, rinse the media trays you have removed, and clean them thoroughly using a toothbrush or scrub pad.

Using these tools will help to get all the algae off everything.

You will also need to clean the filter pads, use your hose or sink faucet to rinse them well.

This step will not affect that all-important beneficial bacteria, as the housing is the component that holds the bacteria. 

Step 8- Take out the Impeller

You will need to be careful with this step, the ceramic ship is very fragile and can break very easily.

So when you remove the impeller from the motor house, you need to carefully and gently remove it.

If you break your impeller, do not worry, there are replacements that you can buy. 

Step 9- Gently Clean the Impeller

This is a very important step. The reason for this is that it can impact how effectively your filter performs.

In fact, the residual dirt can damage your motor.

It is essential to clean the plastic sections around the impeller, this will include the shaft.

Use the toothbrush for this cleaning and make sure that you do not apply too much pressure as this can cause the impeller to break. 

Step 10- Make Sure to Clean the Impeller Hole

For this step, you will need the Q-tip, insert it into the hold the impeller sits in and clean thoroughly.

This part of the filter can make the whole device malfunction and reduce the effective performance of the canister filter.

You would be surprised how much dirt gets inside the impeller hole, so do not skip this step. 

Step 11- Take out the Biological Media Trays

You will need to be quite fast for this step.

When you take your biological media trays, you need to set them aside quickly.

You can put them in a bucket of aquarium water so that the bacteria do not die.

But this is not always necessary.

Remove all the water in the canister filter and throw it away.

Do NOT reuse this water.

The key here is to move fast, as the bacteria can be lost if it is exposed to air for too long. 

Step 12- Clean the Canister

This step is not always needed.

But, if the canister is dirty, you can clean it by rinsing it out with water.

High pressure is better for this part of your canister filter cleaning.

If you want, you can use a cloth to wash off any algae or debris that have gathered in the canister. 

Step 13- Reassemble Everything

You have now completed the cleaning process and can start putting everything back together.

You will need to move quickly.

Make sure to put all the components in their proper place and put the motor housing in place.

Make sure to lock it before you screw all the valves back on and put the pipes in their proper place.

Once again, the key here is to move fast so that the bacteria do not die from exposure to the air. 

Step 14- Turn on the Shutoff Valves and Fill the Canister

Once your valves have been switched back onto the correct position, there will likely be trapped air in the canister.

Because of this, it will not fill up on its own.

You can fill it by lifting the front locking bracket and allowing it to fill up that way before locking the bracket again. 

Step 15- Plug in the Filter

The final step is to plug your canister back into the plug socket.

Before you put the filter back into the aquarium, make sure that everything is functioning as it should. 

Final Thoughts 

That is all for this article, we hope that we have guided you through this process successfully.

You are well on your way to being able to clean a canister filter with our help.

Do not forget, if you have a canister filter that does not adhere to these steps, it would be a good idea to check out the instructions that came with your model. 

With that being said, we hope that you have learned all you need and are more equipped to deal with your canister filter cleaning needs.