Last Updated on February 10, 2023 by Matt

The aquarium filter is the main element in cleaning and purifying your fishes habitat. With plants, fish, crustaceans and all the waste that they produce, the aquarium filter has its work cut out. The filter can get clogged with gunk quite quickly, so it needs to be cleaned regularly. 

There are three parts to most fish tank filters; the mechanical, biological, and chemical filtration media. They are normally found in this order.

In this article we will go over how to clean the aquarium filter. We will give you the information required to successfully clean each of these parts of your filter as well as how often to clean an aquarium filter. 

How To Clean Aquarium Filter


How to Clean the Mechanical Filter

The mechanical filtration media is there to capture the floating debris; pieces of leftover food, fish feces, plants etc from the aquarium water column, and also prevent this from getting to and clogging the other parts of the filter.

First of all it is important to remember you need to use the tank water to clean the filter. Tank water is the ideal, but using RODI water is also acceptable. Your aquarium has a delicate chemical balance, and using regular tap water will upset this balance and stress your fish.

You only need to take a couple of cups of water to use for cleaning, and make sure you don’t get any fish by accident!

If you can take your filter off the tank then you will want to do so, but ensure that you turn off and unplug the filter before you try and take it out to clean it to avoid electric shocks, and a very wet floor!

If you have a bucket to put the filter in it will save your floor as well.

Using the tank water you took out earlier wash the sponge, pad, or whatever your filter has. You want to get rid of most of the debris from the sponge, so squeeze it and rinse it in the water until it is clean. As you are using the tank water you won’t harm the beneficial bacteria.

Remember you can always wear gloves if the sponge is too disgusting! And if you think the sponge is beyond saving then replace it, but don’t change it until you have to. And if your filter uses multiple pads, only change one at a time.

Use the remaining water to clean the casing of your filter. Using a brush makes this easier as you can put some elbow grease into it and give it a good scrub.

You want to give the tubing a good clean as well. Use your brush to get those hard to reach spots.

Once you are done get the filter back together and replace it onto the tank. Or if your filter has multiple stages then read on before putting it back together!

How to Clean the Biological Filter

Be very careful with cleaning the biological filtration media. Beneficial nitrifying and denitrifying bacteria colonize the biological filter which removes ammonia, nitrite, and nitrate from the water column

The last thing you want to do is kill these bacterial colonies. Therefore only use aquarium water when cleaning the biological filter media. Tap water contains harmful chemicals and contaminants such as chlorine which will kill the bacteria. 

All you are wanting to do is to get the scum and filth out from the biological filter. Wash it quickly in the tank water, but don’t overdo it. There will be no need to replace the biological media, such as ceramic rings until they look like they will disintegrate. 

When you do replace biological media, only replace a maximum of a third at once. If you replace more, you risk your tank crashing and ammonia and nitrite levels spiking. The bacteria need to recolonize the new media, and if you do more than a third at once, the remaining bacteria cannot handle the load the aquarium requires.

After cleaning the biological filter, always use a dose of aquarium bacteria supplement, such as API Quick Start or Seachem Stability once the filter is back up and running. This will help recolonize the filter faster.

How to Clean the Chemical Filter

How you go about cleaning the chemical filter will depend on what chemical media your filter uses. 

It is most likely to be an activated carbon filter. Activated carbon is by far the most common chemical filtration media out there. You won’t be able to actually clean this media; once activated carbon has removed pollutants it is done and needs to be changed. So to ensure you still gain the effects you will need to change it regularly about once a week. 

Follow the guidelines for the carbon you have, but you will normally have to change about a third of it at a time, and choose the bits that look worst off.

The recommendations on how to clean other chemical filter media differs depending on the media. Always read the care instructions that are supplied by the manufacturer. 

For example, Seachem Purigen can be cleaned and re-energized using a bleach solution. As the synthetic media adsorb organic waste material, the color changes from white to black. When you put them in a bleach solution, the bleach will remove the organic waste from the media. The color will return to white, and you can rinse them thoroughly and return them to the filter.

How Often Should You Clean a Fish Tank Filter 

how often to clean fish tank filter

Your aquarium filter will get pretty gross, as it spends its time cleaning the water!

As a general rule, you should clean mechanical filters about once a month. If the water is very dirty then clean it more often though. 

You should be doing regular water changes, at least once every week, but you should try and do the filter cleaning a couple days apart from the water change.

The chemical carbon filter will need replacing about every two months as a rule of thumb, but again if the water is looking cloudy then feel free to replace it sooner. 

The biological filter needs cleaning about every couple of months as well. But have a look at it, and if it is clogged with debris then it needs cleaning.

Each tank is a little different, so yours might need cleaning more often than this. Keep an eye on the water quality and you should soon get into a rhythm.  

If your fish are sick or unhealthy then you should definitely be cleaning the filter more regularly to try and get them back in tip top shape as soon as possible.


Hopefully this article has cleared up how to clean an aquarium filter. There are normally three parts to fish tank filters; mechanical media, biological media, and chemical media.

Each of these should be cleaned and maintained in slightly different ways. But with all of them remember to only use tank water! Using tap water will damage fish and plants, while also killing bacteria in the biological filter. 

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