How to set up a canister filter (Step-by-step)

Canister filters are great, they are powerful and you can customize the media according to your needs.

You can use most of the canister filters for freshwater as well as saltwater aquariums.

But setting up canister filters can be intimidating especially if you are a beginner.

No worries in this article I am going to show you how to set up a canister filter step by step.

How to set up a canister filter image

So, first of all, let’s have a look at what you need to set up the canister filters. 

Most canister filter comes with all the essential accessories you will require to set it up.

Also, most of the canister filters come with filter media to get you going.

Just go through the following list you and re-check if all the accessories are available inside the box or not.

Accessories required to set up a canister filter

Besides some canister filters will also come with a spray bar.

Now that we have all the accessories in place, let’s move to set up our canister filter.

Actually, it is very easy to set up a canister filter and it is a very straightforward process.

People get confused in filter media like which filter media should they use and how they should organize the filter media in the canister filter.

But don’t worry in this article I will answer all your questions.

How to set up a Canister Filter (Step-by-Step)

Step: 1

So first of all, separate the motor housing from the canister filter by unlocking the clamps.

Then pull out all the media baskets from the canister filters.

Some canister filters come with only two media baskets some may have two or three.

Step: 2

Now, wash the canister filter compartment with normal water and also rinse all the filter media that you got with the canister filter.

Step: 3

Before putting all media baskets inside the canister filters put only one media basket in the canister filter and see if there is any space left at the bottom. 

If you noticed any gap then you should add ceramic media in that gap. This will prevent filter media foam from getting clogged and it will also provide additional filtration.

Step: 4

Now grab one of the filter media baskets. You are going to put it at the bottom of the canister filter so you should fill it with mechanical filter media.

Canister filters usually come with course foam as a mechanical media. So insert this foam into the media basket and put it inside the canister filter.

To increase the efficiency of filtration you can customize the media basket with three different types of foam (coarse, medium coarse and fine foam).

First of all, put the course media foam insert in the media basket then put a medium course foram insert and fine foam insert in the same media basket.

Doing this way will increase the efficiency of the filtration as the big particles will get removed through the course form and then it will travel up and the more fine particles will get removed by the middle foam insert and the very minute particles will get trapped in the fine foam insert.

If you got a thick coarse media foam insert that is occupying all the space of the media basket then split it into two or get a thin one to make space for other foam inserts.

Remember this customization step is optional. If you are a beginner then I’ll advise you stick with the single corse foam that comes with the canister filter and it works fine.

Step: 5

Now grab the second media basket and fill it with biological media.

Your filter may come with ceramic rings for biological filtration which is perfectly fine to use.

Or you can use bio home as a biological filter media to enhance biological filtration. 

Put the second filter media basket on the first one. Just make sure that the tube of the first media baskets aligns with the tube of the second media basket. 

Step: 6

Then grab the 3rd media basket and fill it with chemical filter media. 

Usually, canister filters come with activated carbon foam insert or activated carbon as chemical filtration media.

So insert them into the media basket and put the basket on the top of the 2nd media basket.

Step: 7

If you have a fourth media basket then you can customize it according to your choice. 

You can fill it up with biological media or chemical media.

Basically, 2-3 media baskets are sufficient for the filtration of an aquarium tank.

Step: 8

To hold the media in and prevent the media from floating around canister filters comes with a tray or guard to put on the top of the last media basket.

So if you got one then put it on the top of the last media basket.

Step: 9

Now it’s time to fit the motor housing.

Put the motor housing on the last media basket. Just make sure that the pipe of the motor housing is aligning with the whole of the media basket.

Now lock all the clamps of the motor housing.

Step: 10

Now it’s time for preparing the tubing for your canister filter.

So grab the tubing you got with the canister filter and cut it according to the length you need.

One thing here to keep in mind is that the ideal place to put the canister filter is below the water tank this is because of gravity.

Gravity helps to pull the water down from the tank into the canister filter and then pump it again in the aquarium.

Also, make sure that the tubing can reach to the canister filter from the aquarium easily and there are not any kinks in it.

Now attach the tube to the input valve of the canister filter and attach intake tubes to the other end which will go into the aquarium tank.

You will see “Inlet” and “outlet” written somewhere around the valves to guide you.

Then attach another tubing to the outlet of the canister filter and the other end of the tubing to the output tubes. 

Step: 11

At this end, you can attach a spray bar if you want and then Mount the output tubing in the tank with vacuum cups.

Step: 12

Now plug in the canister filter. And it’s time for priming the canister filter.

Very few canister filters are self-priming.

Usually, there is a button or knob for priming. 

So press the button or knob a few times.

So now your canister filter should start pumping the water itself. Depending on the canister filter, you will see clear water within 1-2 days.


Wohaa! You made it till the end. I know it’s a very hectic process but it is a one time process and once you figure it out it just becomes easier.

Usually, some mechanisms, especially near the input and output valves vary depending on the brand.

So I have collected some YouTube videos that will help you in setting up your canister filter.

How to maintain canister filter?

Once you set up the canister filter then it will be very easy for you to maintain and clean it. 

You will need to clean the canister filter after every 3 to 6 months. Obviously the more frequently you clean the better.

Basically, the maintenance includes cleaning all the components of canister filter except biological media. 

You should not wash off the biological media because it will remove all the beneficial bacteria from the water that is necessary for a healthy aquarium.

How much is the maintenance of canister filter?

The maintenance of canister filter is very cheap. You will have to change the filter media which is very inexpensive. 

And the best part about canister filters is that you can use any kind of filter media of your choice.

How to install sunsun canister filter

How to install Penn Plax cascade canister filter

How to install Fluval external canister filter.

How to install Eheim canister filter

Hopefully, these videos will help you. 

Let me know if I missed anything or you think any other steps should be added in the article. 

If you found this article helpful be sure to share it.

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Prathmesh Gawai
He is the main author and editor at And he loves to share helpful information on aquarium and/or fishkeeping hobby. Prathmesh has over five years of aquarium and/or fishkeeping experience. Currently, he has a Betta fish tank. He has written hundreds of articles on various aquarium fish species and on fish tank maintenance over the last five years. Connect with him on YouTube here. Learn more about him here.

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