Cleaning your fish tank filter is vital to keep a healthy ecosystem in your aquarium. We have already discussed different filter types, their pros & cons, and many more things. But what about taking care of the filters you already have?

When cleaning the fish tank filter, our goal is to just free all the waste that’s been trapped in the filter and allow it to filter the impurities in the water.Obviously, you may have different brands of filters, but every brand has pretty much the same products for a particular type of filters such as a canister, sponge, or HOB filter.

These different filter types come with different filter media such as filter sponges, Ceramic rings, and bio balls. Let`s go through all the different types of filter media, step by step, and find out how to clean and maintain each without affecting the aquarium ecosystem. 

How often should you clean the filter in a fish tank?

A lot of fish keepers will get into a routine of cleaning out their filter once a week or every two weeks. But some fish keepers that are using larger filters like Canisters or sump filters, can get into a routine of once a month.

Aquarium filter cleaning
Aquarium filter cleaning

If you have a lightly stocked tank with a hang-on-the-back filter, this might be after a month. But if you have a heavily stocked tank with just a couple of sponge filters, you might need to clean your aquarium filter once a week. 

Now you may wonder, how to define the maintenance routine for your aquarium filter. It`s quite easy. 

When to clean the filter in an aquarium?

When you start to notice your fish tank water isn’t looking as crisp as it usually does and you’re seeing debris floating around, it’s time to clean your aquarium filter and do the filter maintenance. 

Debris floating around the aquarium
Debris floating around

This is happening because the sponges and filter media are packed full of debris, and water isn’t flowing through them. It renders the sponge filter pretty much useless. 

Can you clean and reuse aquarium filters?

Of course! You can clean and reuse your aquarium filters. But depending on the condition of the filter media, you can reuse them for limited turners. 

You should change the filter media and filter cartridges from time to time. You can simply refer to the manufacturer’s instructions to find out How long can a certain filter cartridge or filter media can be used. 

Aquarium filter pads
Aquarium filter pads

But you should clean your aquarium filter or change the filter media very carefully as these filters are the breeding grounds for tons of beneficial bacteria that help the aquarium’s Nitrogen cycle

How do you clean an aquarium filter without losing bacteria?

One of the common questions about aquarium filters is that do you need to scrub all the filter and filter media. Well, the answer is no. You should never scrub the filter or filter media to clean out them. 

We know, aquarium filters are places where you get a substantial amount of beneficial bacteria. If you clean the box out spotless every time you maintain the filter, you run the risk of losing your cycle. And this is every fishkeeper’s worst nightmare.

So when cleaning the aquarium filter, just clean or replace the filter cartridges without scrubbing the whole filter. Also when replacing filter cartridges, you can keep one or two old cartridges without replacing them. It helps to establish the bacteria colonies in new cartridges easily.

To remove the nasty mud-like buildup that develops in the filter boxes, just unplug the filter unit, and take the box out entirely from the tank. Make sure not to dump that nasty water into the tank back. 

Once it’s removed, take the water from a bucket that siphoned out of the tank and pour it into the box, swish it around and dump it out. Repeat this process a few times to remove most of that loose debris. 

cleaning aquarium filter box
cleaning aquarium filter box

After that, put the filter back on the tank, put in the cartridge, and fire it back up again. It might sound ridiculous, but it is the best way to save and clean an aquarium filter without losing beneficial bacteria in it. A filter with a little bit of life is always a healthy filter.

The next important thing is how to rinse the filter Media, filter cartridges, and filter sponges. This is where the big debate happens between do you squeeze it out into a bucket or do you rinse it under the sink? 

Can I Clean My Fish Tank Filter and Filter Media with Tap Water?

Squeezing the sponges or filter media out in a bucket full of your aquarium water makes total sense because you don’t have to worry about chlorine in your tap water killing all the bacteria.

Aquarium filter Sponge Cleaning
Aquarium filter Sponge Cleaning

But there’s a downside too. When you squeeze it out in the bucket, the water in the bucket will instantly turn all brown from all the nastiness. Once you release that squeeze, the sponge just sucks up all that debris right into it again.

Therefore, just take your filter to the sink and rinse it out with tap water. Finally, dip it in the aquarium water from your fish tank to wash out Chlorine. I know that sounds preposterous to experience fishkeepers, but it’s going to be fine. The exposure that bacteria gets to the chlorine is minimal, and you’re going to get it much cleaner than you’re doing it in a bucket.

Filter Sponge Cleaning with tap water
Filter Sponge Cleaning with tap water

When to change the fish tank filter?

As we discussed earlier, unless your filter is damaged or malfunctioned you can just replace the filter media and reuse your aquarium filter. Also, it is not recommended to change the aquarium filter frequently as it causes to loss of beneficial bacteria.

But you will need to change your whole aquarium filter when it is damaged or doesn`t function properly. In most cases, the filter pump or power head can malfunction with time.


With the experience, you will be able to familiar with aquarium cleaning and maintenance. Always clean your aquarium filter only when it needs to be clean and never over-clean. The bottom line is that do not create more work for yourself than you need to do. We all love this hobby for the fish, not the work.



I am Prasanjaya who is an aquarium hobbyist for nearly a decade. I wish to help fishkeepers to get accurate and helpful information regarding every aspect of fishkeeping.

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