Last update: November 12, 2022

Biological Filtration – The aquarium filter that is ALIVE!

It’s alive….

Your filter, that is.

And as you will soon learn, that’s a good thing!

A live filter is referred to as biological filtration, and it can make all the difference to the water quality in your aquarium.

Today, I am going to teach you everything you need to know about biological filtration.

What is biological filtration?

Biological filtration is one of three different types of filters that can be used in your aquarium. The other two are mechanical and chemical filtration.

Unlike the other filters, biological filtration uses living organisms to remove nasty substances from your aquarium.

But not just any living organism…


If you are a germophobe, then just the very sight of that word will send shivers down your spine.

But the bacteria used in biological filtration are your friends. If you want to successfully raise happy and healthy fish, you need these bacteria in your tank.

Fishlab Fact: Any filter media that is designed to provide a home to the bacteria used in biological filtration is referred to as a bio filter.

Biological filtration works a little differently from the other methods of filtration. Mechanical and chemical filtration work by removing the unwanted stuff.

But that’s not how biological filtration works… Instead, it converts one chemical to another.

Now this may sound confusing, but it’s actually very simple.

Think back to the nitrogen cycle for a moment. Waste, such as fish poop or uneaten food, breaks down and releases ammonia.

Bacteria then eat the ammonia and convert it to

And then, another type of bacteria converts nitrite to nitrate.

Nitrite converted to nitrate with bacteria in aquarium diagram

This is biological filtration at work.

Biological filtration refers to when bacteria in your tank eat any compound, such as ammonia, nitrite or nitrate, and then convert it into something else.

You want these bacteria in your aquarium. That’s why they are commonly referred to as beneficial bacteria!

With enough beneficial bacteria in your aquarium, they will eat ammonia and nitrite as quickly as it is produced.

What types of bacteria are used in biological filtration?

There are two different categories of bacteria used in biological filtration: nitrifying bacteria and denitrifying bacteria.

1. Nitrifying bacteria

Bacteria that remove ammonia and nitrite from the water

Nitrifying bacteria require a source of oxygen, using it to convert ammonia to nitrite and nitrite to nitrate.

The bacteria can be found on all different surfaces of your aquarium, but where it truly benefits your tank is in your filter media, where it removes ammonia and nitrite from your aquarium as it passes through your filter.

Nitrosomonas – Eat ammonia, converting it to nitrite.

Nitrospira and Nitrobacter – Eat nitrite, converting it to nitrate.

Nitrifying bacteria work together as a team, with one bacteria providing a food source for the next.

A new aquarium doesn’t have enough of these bacteria present to efficiently filter the nasties from your aquarium.

This is the precise reason why you cycle your tank.

During the cycling process you wait for these bacteria to grow in number. Once an established colony of bacteria forms, they will be able to eat ammonia and nitrites as quickly as they are produced.

And once this happens, you can consider your new tank completely cycled.

FishLab Fact: Because biological filtration uses living organisms, care must be taken when cleaning your filter. Using chemical cleaning products or even tap water can kill the bacteria – throwing the nitrogen cycle out of balance and causing chaos in your aquarium.

Nitrifying bacteria grow best on filter media with a large surface area, including…

  • Bio balls
  • Filter floss
  • Sponges
  • Ceramic noodles

2. Denitrifying bacteria

Bacteria that remove nitrates from the water

Denitrifying bacteria exist where there is no oxygen present.

The reason for this is when oxygen is present in water, the bacteria use it to breathe. But without oxygen, these bacteria use nitrates instead, converting them into nitrogen gas[1].

The nitrogen gas then exits your aquarium through the surface water.

Because of this, denitrifying bacteria only exist in areas of your aquarium that are not oxygenated, such as inside rocks.

Filter media that is suitable for denitrifying bacteria include:

  • Volcanic rock
  • Ceramic noodles

For freshwater tanks, denitrifying bacteria will be the least important type of biological filtration in your aquarium – most people skip over it completely.

The reason for this is that nitrates are not as harmful to your fish as ammonia or nitrites. And to top it off, nitrates are removed from your aquarium when you perform a water change.

And because a water change has other benefits, including returning essential minerals to your aquarium, a water change is considered a good substitute to using denitrifying bacteria as biological filtration.

Saltwater tanks are the exception to this. Marine fish, invertebrates and corals all have a low nitrate tolerance – denitryfying bacteria are commonly used to assist in removing nitrates from saltwater tanks.

What is the best biological filter?

Given the correct environment, nitrifying bacteria can grow almost anywhere – even in the filter pad in your HOB filter.

But if you want to achieve the best biological filtration possible, then you want to use a filter media designed for housing bacteria.

And to do that, it’s all about the surface area.

Did you know? When discussed online, “biological filtration media” is often shortened to bio media.

You see, the more surface there is for bacteria to cling to, the more biological filtration you can achieve.

Think the filter media as a house. A single bedroom apartment won’t fit as many people inside it as a mansion.

Filter media designed for biological filtration is essentially a mansion for beneficial bacteria.

Let’s take a closer look at some of the best and most popular bio filters around.

Ceramic rings

Siporax sintered glass biological filter media

Suitable for both nitrifying and denitrifying bacteria

It’s no secret that my personal favorite biological filter media is Siporax. Made in Germany, this may look like any other ceramic ring, but it’s actually made from a sintered glass.

I have had these in my aquarium for a year and a half now – I just give them a rinse every 6 months at the same time I perform a water change. Just make sure to rinse them in tank water!

Ceramic balls

Cermedia MarinePure ceramic balls for biological filtration

Suitable for both nitrifying and denitrifying bacteria

Ceramic is another popular biological filter media, and one of the best comes from MarinePure. Proof that big things come in small packages, each ceramic sphere can contain up to 240 square feet of surface area!

Bio balls

Closeup of black plastic bio ball open structure

Suitable only for nitrifying bacteria

Bio balls are a plastic bio media that often gets a bad rap. However, they are more than capable of providing biological filtration without issues when used correctly.

The key to success with bio balls is having a mechanical pre-filter so that waste does not get stuck in the holes of this media.

Moving bed filter media

Moving bed filter reactor bio media

Suitable only for nitrifying bacteria

Last but not least, I want to touch on a bio media made for a specific type of filter – the moving bed filter.

You may have noticed that these pieces of media have a rather small surface area when compared to the other media I discussed.

That’s because each piece of filter media is constantly moving, crashing into one another. The idea is that only the strongest bacteria can cling to the surface and filter your tank. Any dead bacteria falls off, allowing live bacteria to take its place.


When used correctly, biological filtration is a major contributor to the health of your aquarium.

Just remember that bio media is essentially a living creature and can die if not cared for. When cleaning your bio media, only rinse it in tank water – using tap water can kill the good bacteria due to the chlorine content.

Do you use biological filtration in your aquarium? Have something to add? Let me know in the comments below!

Ian Sterling

I've been keeping fish for over 30 years and currently have 4 different aquariums – it's an addiction. I'm here to teach you everything there is to know about fishkeeping.

I also use this site as an excuse to spend lots of money on testing and reviewing different aquarium products! You can find my reviews here.

Comments (36)

Thank you for the explanation. I found out my tank was not cycling because I didn’t include any media inside my filter.

Hi Jaldin,

Oops! Don’t worry about it, we all made mistakes when we first started. It gets easier from here!

Is it safe to “swish” bio media in aged, filtered water I keep in a drum, or, is actual aquarium water

Hi Woody,

I prefer water from the tank because it’s fool proof. Your beneficial bacteria is already happily living inside it, so you can be sure your tank water won’t kill it, which would require you to cycle your tank again.

I cannot comment on the safety of your aged filtered water, but it could still have chloramine and other contaminants. Personally, I wouldn’t risk it.

I have a Fluval FX6 for a 45 gallon overstocked tank (discus and tetras). Once my tank cycles, can I stop using chemical filtration?

Hi Laurie,

It would all depend on what chemical filter media you are using and why. Activated carbon,zeolite and other resins are all designed to remove specific things from your aquarium. Even so, only you will be able to answer this question based on water testing with an aquarium test kit, after cycling has completed.

Hi Lauri,

Since Siporax has come back on the market, I have not swapped it out. That isn’t to say I won’t ever change it – if I feel it is no longer holding beneficial bacteria (using water tests as an indicator) or it looks like it is starting to smooth (rough surfaces hold more beneficial bacteria) I may consider it. Like ceramic rings, they probably won’t last forever, but at this stage I foresee many years of use to come.

I have had aquariums since about 10 years old. I bought a 32 bio tank. I am trying to go brackish. After four or so months without living critters. How do I get rid of the skumm attaching to my glass? It looks like a pieces of glad wrap. I want to get some fish from a coop, but not with this. I put a skimmer in the middle compartment.

Hi Gerri,

I’m having trouble picturing what algae/scum that could be. If you wipe it down, does it return?

I am using a AFM glass media as a floating bed what I would like to know what flow rate though the bed is required
Any advise would be great

Hi Tony,

Unfortunately, I have no experience with AFM glass media. You would be best served either contacting the manufacturer or making a post on an online aquarium forum – it’s possible someone who uses AFM media in a similar application will be able to answer your question.

I have two Nu clear canister filters on my 185 gal fresh water tank. The first canister has a cartridge to serve as a mechanical filter. The second canister is filled with bio balls to serve as biological filter. I am in the process of changing out the bio balls I know I should not change all the bio balls at one time. I will change approximately half the bio balls and add the new material. How long should I run the new ceramic rings to allow them toget a good charge before changing out the second half. Thank you very much for your assistance,

Hi Wayne,

When swapping out old deteriorated rings, I do half at a time for 2-3 weeks before swapping out the other half. I have never had an issue with ammonia spikes with this length of time. I have no first-hand experience swapping out bioballs to ceramic rings but would expect the process to be very similar. Just make sure that when you add your new biomedia, you place it in a filter media bag. You can even layer it in multiple media bags if you want. This will make the next time you replace them (or clean) a much easier task. Years from now, your future self will thank you.

i find crushed coral fantastic as a media in a live bearer tank i also use it in one of my internal filters with a small piece of sponge near the propeller i dont clean the corral on the bottom of the tank as im afraid to kill the bacteria it is heavily planted 55 gall tank plants grow great with meidium lighting i use iron pottasium and mineral nuitriants but no orther fertiliser feeds etc

Hi Chris,

Thanks for sharing your feedback. Crushed coral is also good, but given it’s more difficult to come across and more expensive than ceramic rings, it’s not as popular. It sounds like you have an amazing tank!

Hi Ian:

We are thinking about putting a moss ball in our betta’s tank. I’ve read good things about it being a natural filter, but also bad things about it messing up the water.

What is your opinion, please?


Hi Lezlee,

If you are maintaining your tank properly (cleaning, testing the water) and monitoring the moss ball so that if it dies, it is removed before it rots, there is nothing wrong with adding one. It’s an extra piece of scenery for your betta to interact with. Like with any plant you add to your aquarium, if it isn’t cared for, then it can cause problems – but I see them as no issue for any fishkeeper who is actively involved in their tank.

Thanks Ian! We are certainly keeping our tanks clean and tested…sometimes it seems like that’s all we do…lol!

I have a 120 gallon fresh water tank ang I have 9 koi around 7” long. I recently cleaned my tank and all my filter media with tap water. (Big mistake). Now my Amonia level is off the charts. I did another 50% water change and still high. i also tried the Seachem AMGuard and still too high. I will put more bio media and hoepfullyw will cure this. My Nitrite and Nitrate are both normal. How long will my new bio media becomes fully established and when will my amonia drop to normal?

Hi Jerome,

A 120 gallon tank is too small for that many koi, especially at 7 inches long. Koi are pond fish – they need a lot of room. This is the biggest reason why your ammonia instantly spiked off the charts.

But to answer your question, you will essentially need to cycle your tank again, doing a fish in cycle. Your nitrite and nitrate likely read normal because they have stalled. I would expect both of these to spike as the cycle progresses.

Hi Ian, loving reading your blogs.

Am I right in thinking that the bacteria live on a surface (for example ceramic rings in the filter itself) as opposed to free floating in the actual water?

The reason I ask is because we’re currently mid cycle and nitrates are getting fairly high so I want to do a water chance to keep on top of them but, if I do a 50% water change, could I be removing 50% of the bacteria? Or is that not the case with them residing mainly on surfaces?

Thanks 🙂


Hi Stuart,

Your thinking is spot-on. Beneficial bacteria are clingers and hide on the surface and in the pores of your biomedia. Performing a water change correctly will not impact your cycle. In fact, water changes are an essential part of fish-in cycling.

Are we ever supposed to change the media in a moving bed filter?
My media has been turning brownish. Should I leave it working as is,meaning, is that the color of the working bacteria?
Vic F.

Hi Vic,

It all depends on how gunked up it is. If it’s just a light coating, it’s likely fine. If you have been running this for years, then it’s possible they need a clean. Moving beds do have a habit of accumulating gunk at the bottom though, which does need to be cleaned as it builds up.

Hi Ian,

I am new the shrimp keeping and have a 5g aquarium. I currently have 2 Bloody Mary shrimp and my water parameters are as follows:
Ammonia: .25
Ph: 7.6
Nitrite: 0
Nitrate : 10-20ppm (can’t tell in test kit)

How can I get my ammonia lower? Is it affecting my shrimp?

Hi Brandon,

That all looks really positive. Are you testing your water and reading the results in natural daylight? I only ask as indoor lighting can make the results look off and that 0.25 ammonia might not even be there. I only say this since given your 0 nitrite and 10-20ppm of nitrate, it appears the tank is cycled. Can you test again and confirm this?

I have new small ras system. Biological filter has lawyer of ball and layer of ceramic. I start directly. I put fish and start running system for first time. Filter does not remove Ammonia… Very very high level of Ammonia..
How can i manage biological filter correctly

Thank you very much for your use full Information
I have new biological filter in ras filter for talipia supplier told me density 100 kg per one cubic metre.
But i donot know how to start it.
Can i use it directly or need preparation time before putting seeds.
My regards

Dear ian, thanks very much for your help.
Can you please tell me how can i manage biofloc fish farm for talipia and what available density
My regards

Hi Abdo,

Unfortunately, I cannot help you here, I am not the right person to speak to regarding aquaculture and fish farming. My knowledge is best is limited to the smaller enclosed systems you see in aquariums.

Hi my friend
Sorry for disturbing you. I have a question which is better thanks outdoor or indoor in ras system??
What is the Best tank design for talipia ras system
Thank you for your precious help

Hi Abdo,

As per my last comment, I cannot help you with aquaculture related questions.

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