How to Clean an Aquarium Filter

How To Clean An Aquarium Filter

The aquarium filter is an indispensable component of an aquarium setup. It does a tremendous job at keeping the tank nitrogen cycle stable, therefore, making the environment safe, healthy, and habitable for aquatic life-forms.

Regular cleaning of the aquarium filter is an effective way to ensure that it remains in good condition to function optimally, thus make efforts to clean your filter as you clean the aquarium’s interior. Luckily the whole process is rather straightforward and simple.

In a nutshell, to clean the aquarium filter, fill a bucket with tank water and put the filter media into it, squeeze it, and then put it back – that way any gunk you just dislodged goes into the old water you are about to remove anyway. Bear in mind that you do not have to perform a complete clean-out.

This article explains the procedure involved in cleaning an aquarium filter to maximize its effectiveness and performance, in addition to the frequency of filter cleaning and some tips from the experience.

Why Should We Clean Aquarium Filters

Even though there is no consensus on when we should clean the aquarium filter as the timing differs between setups, all experienced aquarists will tell you that not cleaning a filter is just a really good way to kill a lot of fish or shrimp.

Now, one is expected to clean the filter media when it gets clogged. In this state, it will become more difficult for water to flow through it as required. Also, the particulate waste trapped in the filter material will limit its ability to trap new dirt.

Anyway, before we go into this, let’s briefly highlight the types of aquarium filtration.

Interesting fact: It is very possible to run a tank even without a filter. However, in this case, it will require a species setup. You can read more about it in my article “No Water Change Tank?! Top Offs vs Water Change”.

–         Mechanical filter:

This is the part of the aquarium filtration system responsible for trapping suspended particles of dirt and debris hence making the water clearer. This filter also grasps a considerable quantity of beneficial bacteria. The bacteria help in establishing a balance by breaking down ammonia into nitrites and nitrites into the less harmful nitrates.

The mechanical filter is ideally a sponge or filter floss (filter pad/filter wool) available in a variety of pore sizes.
This media is usually placed next to the chemical filter in the filter compartment.

–         Chemical filter:

The chemical filter works by adsorbing medications, foul odors, dissolved chemicals, and pollutants from the aquarium water.

Activated carbon is the most commonly utilized chemical media, there are others too, for instance, resins formulated to target a specific substance in the aquarium water.

–         Biological filter:

The biological filter media provides a large, porous surface area to accommodate colonies of beneficial bacteria. These include bio balls, bio rings, ceramic rings/boxes, and other similar products that fit into the filter compartment to provide a site for bacteria populations to grow.

Normally, this filter goes below the chemical and mechanical filter.

When to Clean the Aquarium Filter

  • Mechanical filtration. If you are using a sponge filter in your aquarium, rinse it every 1 – 2 months or whenever you notice a great deal of gunk on the surface.
  • Chemical filtration. The carbon media should be promptly replaced when it becomes saturated, usually a month after placement.
  • Biological filtration. It is usually recommended to clean bio-media every 6-8 months.

If your filter has more than one type of filtration – never clean them at the same time. This is just in case if something goes wrong.

If you are using filter cartridges just take it out and put a new one following the instructions on the back. There is no need to clean it. Do not change all cartridges at once, it may cause a mini-cycle.

Note: Mini-cycle is the result of an insufficient amount of beneficial bacteria compared to the existing bioload in the tank.

How to Clean the Aquarium Filter

It all depends on how your tank is set up. Nonetheless, here’s how you can do that:

1. Turn off the aquarium filter before any filter maintenance activity.

2. Take out the mechanical filter media (sponger or filter pad).

The bag trick: It is relatively easy to take filter media if you have a hang on the back or canister filter. However, if you are using a sponge filter, spread a clean, thin polythene bag over the filter and take it out of the tank.

The essence of initial covering with the bag is to prevent debris on the sponge filter from scattering all over the aquarium water during removal.

3. Pour water in a clean bucket.

Pour water in a clean bucket, preferably water from the aquarium using a siphon, or just scoop out water with a clean bowl.

Note: You cannot use buckets made out of zinc, aluminum, or copper. Water will come into reaction with these elements causing an imbalance. It must be a special bucket for the aquarium or made out of plastic at least.
Important: Do not use soap, detergents, or bleach to clean your filter media, it will definitely kill your beneficial bacteria.

4. Clean Filter media.

Water after cleaning aquarium filter
water after cleaning the aquarium filter

Immerse the filter media into the bucket of water and give it a few squeezes to release the gunk off the surface.

Note: Filter media is designed to trap finer particles, and it gets dirty from accumulating a large mass, so you have to rinse it thoroughly to get rid of the waste.

Do not clean all of your media at once if you can avoid it.

Take out one sponge or pad and rinse, then during the next maintenance period, you can clean the other. It will reduce the risk of harming the beneficial bacteria, disrupting this cycle and thus killing your fish.

Important: Frequent cleaning or replacing filter media may crash the tank. Instead, filters should only be rinsed gently in tank water to preserve brown gunk while removing loose debris. Thick, dark brown biofilm indicates an optimally functioning filter.

5. Rinse it several times.

The water usually turns a dark brown color. Don’t overthink and don’t be overzealous as some people do. The whole process of squeezing and rinsing filter media usually takes around 30 seconds.

6. Replace water

Rinse it a few times more till it’s visibly clean.

7. Scrub the casing and tubes.

You can use the leftover water in the bucket or tap water to clean the other parts of the filter.

8. Insert the filter media back into the filter compartment of your HOB, canister filter, or reassemble it, if it is a sponge filter.

9. Test your water

Next 2 days check your ammonia and nitrite levels to make sure you did not upset the nitrogen

Test kit – link check the price on Amazon.

Is it Safe for Filter Media?

Keep in mind that this media can also get ruined easily because of the soft material it’s made from. That said, replace it when it loses its form and can no longer be cleaned like before.

The filter sponge is suited for prolonged usage and does not need to be replaced regularly.

Moving on to the biological filter media, it requires cleaning only when the porous surface area becomes blocked with solid debris. The surface of this media usually takes longer to clog when there is proper mechanical filtration.

If necessary to clean this, rinse the media in a bucket of tank water to dislodge the debris. This should be done gently to maintain the bacteria colonies.

Is it Safe for Beneficial Bacteria?

I have seen countless posts on forums, Facebook groups, etc. that rinsing filter media rigorously will eliminate a great deal of the beneficial bacteria, thus prompting the new tank syndrome or mini-cycle.

Some hobbyists even recommend never squeeze the filter media during cleaning but instead basically bang it on the sides of your bucket.

Do not listen to this! This is a myth.

It is no possible to over-clean the filter by simple squeezes for a few seconds.

When should I Change the Filter Media?

After a while, the filter media will get worn out, and it won’t remove dirt particles like it used to.

Depending on the kind of filtration system, you can notice a decrease in the flow rate of the filter.

The best course of action is to replace the old media with a new one so that proper filtration will continue in the aquarium.

The current form of the filter media will dictate if there is a need for a replacement.

  • Filter floss needs to be replaced more often since it easily disfigures and clogs faster. Therefore, it must be replaced regularly. Depending on the manufacturers, generally, a few weeks from the first usage.
  • The sponge can easily stay for several months before needing a replacement (according to manufacturers). In reality, you can keep them for years! Basically, you only replace sponges if they are falling apart.
  • The biological filter media does not need to be replaced unless there is severe damage. When this occurs, insert a new filter media into the unit and wait for it to accumulate beneficial bacteria colonies before removing the impaired one.

This filter doesn’t absorb/adsorb impurities like the other filters, so there is no need to clean or replace it regularly.

  • Carbon and chemical media should be replaced once a month.

The chemical filter (carbon) gets exhausted quickly, so it should be replaced regularly. Prolonged usage will cause it to stop adsorbing impurities hence switching its role to a biological filter media by providing a porous surface for attachment of beneficial bacteria populations.

The replacement can be extended a bit further if the media isn’t too clogged. Don’t attempt to clean or “recharge” exhausted activated carbon, simply get a fresh one instead and add it to your filtration unit.

You can read more about it in my article “Everything about Aquarium Activated Carbon”.

How to Prepare a New Filter Media?

Filter media holds a substantial mass of beneficial bacteria. Therefore, it’s good practice to alternate cleaning or changing the mechanical filter media to avoid losing all the attached beneficial bacteria at once.

DO NOT change/replace filter media without preparation! If you see that soon you will have to replace filter media:

  • Add a new sponge or pad to the existing one.
  • Install the second filter in the main tank, if it is possible.

I’d recommend doing that at least 2 weeks before the replacement. This time will be enough for bacterial colonization in the new filter media.

Changing the Filter Media and Doing Water Changes

Some people say that you should not do filter maintenance on the same day as a water change. There should be some kind of a gap for 3-5 days.

This is a popular misconception that beneficial bacteria also exist in the water column of the tank. So, by doing a water change and cleaning filter we increase the risk of removing too much beneficial bacteria from the tank.

This is wrong.

Every surface you have within your tank targets for bacterial growth. It is on the décor, live or fake plants, driftwood, rocks, tubes, heaters, glass, substrate, and, of course, in the filter of your tank.

| Beneficial bacteria do not exist in the water column of the tank!

That is why doing filter maintenance at the same time as a water change will not cause any problems for the tank.

On the contrary, this is exactly what we should do because it is convenient and saves a lot of time. Therefore, I do not see any reason for splitting them by a few days or something.

Can I Clean Filter Media in Tap Water?

How To Clean An Aquarium Filter (sponge) with tap waterYes, you can clean it with tap water as long as you dechlorinate it!

I bet that this is the most popular answer you will get if you type it in Google.

However, this is not like that. Many things, we were told when we started in this hobby, are outdated now. 

Generally, the idea that chlorine and chloramine will kill beneficial bacteria comes from water changes. When we prepare water for water changes we let it age for a day of two (Chlorine will usually evaporate out of water within 24 hours). 

As a result, other hobbyists came to a simple conclusion that they also have to do the same when rinsing the filter media.

Well, it is true that we need to use de-chlorinated water because our animals (fish, shrimp, crayfish, etc.) have to sit in this water all the time.

However, it takes like 30 seconds to rinse your media. So, it will not sterilize your filter media in that time.

There is a very interesting post about it on fishlore.

So, whether you can use tap water to clean your filter media and the answer is yes.

Note: Keep in mind that the temperature of the tap water should not be too cold or hot. Ideally, make sure that the temperature is the same as in your tank.


Even though I have not had any problems with tap water myself, I still cannot recommend it to everyone.

So far there are no scientific studies that can help us to know more about how chlorine affects beneficial bacteria. Personally, I could not find any.

Basically, we do not know what concentration of chlorine is enough to do any kind of harm (if any) to nitrifying bacteria. We do not know exactly how much time it takes to harm beneficial bacteria as well. In addition, we all have different water in our locations.

So, why some of us take this ‘unnecessary risk’?

The most important factor here is how good the balance in the tank.

For example, in an established tank, there will be a lot of bacteria on other surfaces to deal with the repopulation, in case you lose some part of it during cleaning. However, for a new tank, it may crash the cycle, in the worst-case scenario.

Therefore, if you are a beginner and want to play safe, it will be better to use the old time-tested method – tank water.

Dirty Water is Awesome!

Do not waste that dirty water after you clean everything. This water contains a lot of nutrients! This is amazing stuff for your indoor and outdoor plants! Excellent fertilizer. Your plants will love it!

Actually, people pay money for it and you get it for free. 🙂 

In Conclusion

A clean aquarium filter goes a long way in ensuring the overall cleanliness and stability of your tank. In this regard, draft and stick to a proper cleaning routine to keep the filters clean. Following the guide — clean the media properly and replace it when necessary.

The condition of the filter can affect the health of your aquarium drastically, and there is no justifiable reason why any aquarium owner should fail to take adequate care of the aquarium filters — knowing fully well that it has an enormous impact on the clarity, chemistry, and quality of the tank water which equally dictates the health of your aquarium fish and inverts.

Ultimately, having an efficient filtration system should be top-priority if you really want the tank inhabitants to thrive and your aquarium to keep running smoothly.

Related articles:

Leave a Reply

Your email address will not be published. Required fields are marked *

Recent Content