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How to Clean Aquarium Filter Without Killing Bacteria in It?

Taking care of a fish tank is a big deal, and one of the most important quests is to find out how to clean the aquarium filter without killing bacteria. Yes, the word bacteria is …

clean aquarium filter

Taking care of a fish tank is a big deal, and one of the most important quests is to find out how to clean the aquarium filter without killing bacteria. Yes, the word bacteria is not always associated with good things, but they are good helpers when it comes to your aquarium.

How to Clean Aquarium Filter Without Killing Bacteria?
To clean your aquarium filter without killing bacteria in it, you’ll need to first remove the filter from the tank and then rinse it in old tank water. Be sure to remove any debris from the filter before putting it back in the tank.

The Ecosystem of Your Fish Tank

Follow these simple steps to preserve the bacteria while cleaning the aquarium filter:

  • Rinse the filter in clean water

clean aquarium filter

  • Ensure that the water that you use isn’t too hot or cold

remove the dirty filter

  • Don’t use aggressive chemicals when cleaning the filter.

the filter was rinsed

Are there any bacteria?

Bacteria are a vital part of the circle of life. Even in the forest, parks, and little ponds, they fulfill the role of natural cleaners and decompose any possible waste left by other organisms. They break down organic matter and then turn it into minerals and compounds that plants can use to start photosynthesis.

Just like that, bacteria also work in your fish tank. Their main role stands in the cycle of nitrogen which can become toxic when it builds up in the aquarium. Different species break down nitrite that comes from ammonia in fish excrement. You can introduce a colony of good bacteria in several ways, and then it will gradually get accustomed to the filter of your tank.

Moreover, they will clean the food leftovers and any dead plants that might ruin the ecosystem of the aquarium. These natural helpers balance the amount of organic matter residing in the water. Bacteria can even get rid of the yellowish tint on the walls of the glass, which usually builds up from the excess waste.

It is beneficial to have bacteria in your fish tank since it will clear the water in the environment. You don’t want your fish to get intoxicated by the organic waste. In addition, too much matter in the aquarium can decrease levels of oxygen, which can negatively affect the fish.

Nevertheless, there are some dangerous strains of bacteria that may appear in your tank, so it’s important to be aware of that. That is why regular cleaning is an absolute necessity.

What if I lose it?

First of all, if you overdo the cleaning, you can accidentally get rid of all of the bacteria, both good and bad. Of course, it is important to keep an eye out for any possible threats to your pets, but you still need to understand that bacteria are a vital part of the ecosystem. If you take out one stage of the decaying cycle in the tank, it can have negative results, like nitrite poisoning.

In addition, if you don’t have bacteria in your filter, it won’t be as effective in cleaning all of the water in the tank. Most of the time, fish owners add bacterial colonies that you can buy in pet shops. They live in the sponge and help process small particles going through the filter.

Please note that it is better to avoid cleaning your filter with different chemicals because they can potentially kill good bacteria and afterward affect the health of your fish.

Be careful with your cleaning

If you are worried that you can accidentally kill all of the bacteria in your filter, you should follow some important rules. First, don’t clean your aquarium too often. Of course, it depends on the size of your tank, the number of creatures living in it, and the power of the filter.

“How to clean the fish tank filter without losing bacteria,” you might wonder. Your filter consists of filter pads or a sponge. The basic part is that you need to rinse the parts of the filter in cool, clear water from the other tank that has been previously cleaned. It is important not to make the water too cold or too hot because it can affect the bacteria that live in your filter.

How to clean the aquarium sponge filter? Well, as with any sponge that you might have in your house, you need to give it a few squeezes. Pay attention while you do that, as when you see that there is no dirt leaking through the sponge, that means it is all ready to go in the tank. Sponge filters hold a lot of beneficial bacteria, and they are a good choice for your aquarium.

As for how to clean an aquarium filter pad, the process here is a bit different. Filter pads need to be changed more often, as they hold a lot of dirt and eventually stop filtering. To clean them, you need to rinse them in clear water a few times, squeeze them, and then roll them between your hands. If you notice that they don’t get any cleaner, then it is time to replace them with new ones.

FAQ on Bacteria Safe Cleaning

Knowing that there are bacteria in your tank might be scary, but bacteria are an important part of your fish tank. To put your mind at ease, we have compiled a list of the most common questions that people ask about this subject.

How often should you clean the filter?

It all depends on the size of your aquarium and parts of the filter you have. It is better to regularly check how dirty it is and then decide whether you should clean it or not. Most filters require cleaning once every two weeks.

How often should you change the filter?

Since there are different parts within your filter, you need to know that there are two main parts to replace: a sponge and filter pads. Filter pads require regular changing, but sponges can last for much longer. You need to pay attention to all of the parts of the filter to be sure that the environment of the tank is healthy and clean.

Also read:

Be Friends with the Bacteria in Your Fish Tank

All in all, bacteria are an important part of your tank, and you need to be aware of their existence. Cleaning your filter should be a regular task, and don’t forget to be careful with how you treat your ecosystem. Your fish require a lot of attention, and if you keep them healthy, they will definitely be happy.

How often do you clean your filter? What tips on keeping the tank clean have you found? Please, let us know your opinion in the comments below.


  • How natural can the seawater in a large inland aquarium be? A bacterial study at Georgia Aquarium gives scientists a good sign (by Ben Brumfield, Published Oct. 23, 2018)
  • Diversity of bacterial populations in recirculating marine aquarium with different marine ornamental fishes (by Thavasi Renga Thavasi – Private Biotech Company in Wisconsin, USA)
  • A controlled aquarium system and approach to study the role of sponge-bacteria interactions using Aplysilla rosea and Vibrio natriegens (by Mohammad F. Mehbub, Jason E. Tanner, Stephen J. Barnett, Jan Bekker, Christopher M. M. Franco & Wei Zhang)

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