Cleaning the aquarium filter: what do I have to consider when cleaning the aquarium pump?

Once your aquarium has been set up, the care of your tank begins. In addition to the weekly partial water change, the aquarium filter must also be cleaned from time to time. However, the Aquarium Filter is one of the most important objects in the aquarium. After all, irreplaceable microorganisms that convert harmful ammonia into nitrate and thus directly contribute to the well-being of your aquarium inhabitants stay there for the equilibrium in the tank. What you have to consider when cleaning your tank filter and how often you should clean the aquarium pump you will learn in the following article!

Table of Contents

Why you need to clean an aquarium filter

In your aquarium filter you will usually find a combination of mechanical and biological filter media – for example sponges but also certain minerals. Even if biological sounds like nature and many an aquarist might believe that an aquarium pump does not have to be cleaned with biological filter media, an aquarium filter needs to be cleaned after a certain time, regardless of whether it is equipped with mechanical or biological filter media. This is simply because the filter media not only collect useful microorganisms, which are irreplaceable for the equilibrium in the aquarium, but also dirt particles. Too much filter sponge in the filter media reduces the flow rate in the aquarium filter. This ultimately leads to less and less water being cleaned/rolled per hour, which in turn leads to noticeably faster pollution in the aquarium, in particular to an increased proportion of ammonia. When cleaning your aquarium filter, you will need to remove this excess filter sludge to ensure that your pump is working at a constant rate.

Cleaning the aquarium filter

Why should I be careful when cleaning the Aquarium Filter?

In general, when cleaning the filter, you should remember that there are various useful microorganisms within the filter media that are of great importance for the well-being of your aquarium inhabitants. You have probably already heard of the nitrite peak, which can be observed in the early days of a newly established aquarium: this is caused, among other things, by the fact that these useful bacteria have not yet formed in a newly established aquarium. The microorganisms that inhabit the Aquarium Filter are significantly involved in the degradation of nitrite (nitrification), which in high doses can be fatal for aquarium fish. To avoid the formation of a high nitrite content in the aquarium, you should never remove too much filter sludge from your filter.

How often should I clean my aquarium filter?

As described above, irreplaceable bacteria are living in your aquarium filters for the aquarium, which are significantly involved in the degradation of nitrite. In order to avoid damaging the bacteria so much that an excess of toxins can be produced, which could be fatal for your aquarium inhabitants, you should not clean your aquarium too often. In general, small internal filters such as those frequently found in smaller 54-60 litre aquariums or nanoaquariums require more frequent cleaning, while external filters (often present in larger aquariums) require less frequent cleaning. Cleaning is generally necessary when the flow rate of your aquarium pump has already decreased significantly (less than 70%-60% of the normal flow rate) and there is a lot of filter sludge in the filter media compartment.

  • With small internal filters, this can already take place after 1-2 months after the last cleaning.
  • A large external filter, which is often used in 180-240 litre aquariums, can also do without cleaning for 6 months – depending on the model.

Cleaning the aquarium filter

How to clean an aquarium filter?

Preface: In general, you should only clean your aquarium filter during your weekly partial water change. I wouldn’t recommend cleaning your aquarium filter under running water, as you will destroy too many useful bacteria so quickly.

  • First, take your aquarium filter off the power to avoid damaging the motor of the pump, which can happen if the impeller runs without adding water.
  • During the partial water change, depending on the size of your filter, you leave one or two buckets of the extracted water from your tank in a bucket – this is required for cleaning your aquarium filter.
  • When disassembling your aquarium filter, you should pay attention to the order of the filter media and sponges: some internal filters only work properly if the filter media are correctly aligned.
  • Now clean your filter media and the sponges in the extracted aquarium water. You should clean the filter media of coarse dirt by rinsing them several times through the water and squeezing them out so that the coarse filter sludge dissolves. Do not forget to remove dirt from the Aquarium Filter housing and the filter media compartment.
  • Now it goes to the filter pump where you should be particularly careful: there are many small parts that you can quickly damage during cleaning. In order to get to the filter pump one usually loosens a kind of magnet which holds the rotor in the housing. Now you can easily remove the coarse dirt from the rotor with a toothbrush and crêpe paper. The inner wall in which the rotor/impeller is mounted is best cleaned with an aquarium tube brush, which you can buy for small money from Amazon:


Be careful with used tube brushes: make sure that they do not come into contact with detergents or other chemicals. Even the smallest amount of chemicals entering the aquarium filter can disrupt the overall biological balance in your tank and lead to the death of the fish.

  • If you have cleaned all parts of your aquarium filter you should check the filter media and the sponges. If, for example, the sponges are deformed or fall apart (strong traces of use), you can renew them. When it comes to the shelf life of filter media, you should generally follow the manufacturer’s instructions for use. Filter media can be purchased for little money in pet shops. If you replace filter media or sponges you should dip them into the water you just cleaned the aquarium filter with. This allows the sponge/filter media to absorb part of the filter sludge, preventing the microcultures in the filter from dying.
  • Then put your aquarium filter back together in the correct order – as mentioned above, this is especially important for the filter media/sponges, as some aquarium pumps only work properly with the correct composition.
  • Now the aquarium filter is filled again with water and can be switched on again as soon as the partial water change has been carried out, i.e. the water in the aquarium has been refilled.

Cleaning the aquarium filter

The following should be observed and avoided when cleaning the Aquarium Filter

The aquarium filter is one of the most important objects in the aquarium because it contains important microorganisms that are responsible for nitrification, i.e. the conversion of ammonia to nitrate. In order to avoid damaging the microorganisms during cleaning, you should completely avoid the following.

  • Never clean your aquarium filter with chemicals or detergent as this will harm all aquarium inhabitants.
  • Always wash your hands before cleaning your Aquarium Filter. In this way you avoid the contamination and remnants of soap getting into the aquarium water.
  • Do not clean your aquarium filter under running water at the tap. The best way to clean water is to use the aquarium water that has been sucked off, because this will ensure that your microorganisms do not die off in the pump – logically, they will also stay in the aquarium water.
  • Do not clean your aquarium filter completely. You should only roughly remove the filter sludge and not damage the important filter bacteria by destroying large parts of the cultures. That’s another reason: clean your filter with extracted aquarium water. This way you can usually not clean your aquarium filter so much anyway that your filter bacteria will be destroyed.
  • Do not clean your filter too often. As I said, sometimes the worst thing that can happen to your aquarium inhabitant is a nitrite peak that can occur without useful bacteria.

Cleaning the aquarium filter

Conclusion: cleaning the aquarium filter is not difficult

Of course the cleaning of your aquarium filter is a somewhat more complex matter than simply to carry out the weekly partial water change, after all you have to pay attention to some things. However, if you value the above steps and avoid what I have written down for you, nothing can go wrong anymore.

TIP: An external filter is not only much less conspicuous in the aquarium, because most parts of the filter are not visible in it, it also has to be cleaned much less frequently, because a combination of biological and mechanical filter media gives it a much better cleaning power. You can purchase your external aquarium filter on Amazon and support this project with your purchase – thank you very much!

Cleaning the aquarium filter: what do I have to consider when cleaning the aquarium pump?

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