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What is a Biofilter in Aquaponics?

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One of the most important parts of your aquaponics setup to monitor and maintain is the quality of the water in your system. As aquaponics is a system based in and around water, keeping the water to a clean, usable standard is an easy decision to make. And the device in charge of regulating the water level, together with housing the beneficial bacteria, is known as the biofilter.

When fish excrete waste into an aquaponics fish tank, this waste is converted into bioavailable plant food (this is the core component of the nitrogen cycle) this converted waste is then accessible to the plants you have growing in your system  

However, this waste can build up in the system and potentially turn it toxic. Possibly killing your plants and fish and undoing all your great work.

This is where to role of biofiltration comes in. Having a biofilter effectively gives the bacteria needed to create that nutrient-rich plant food a home and workshop to live and work in.

In this article, we will expand on what a biofilter is, how it works, and if you need one for your aquaponics setup. is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for us to earn fees by linking to and affiliated sites. As an Amazon Associate, I earn from qualifying purchases.

What is a biofilter?

A biofilter is an integral part of your aquaponics system. They are biological filters made out of non-corroding and ideally light materials. Made from many types of materials such as clay, plastic, and fiberglass.

Specifically designed to promote the development of bacteria essential to the aquaponic nitrogen cycle. Biofilter media are used to provide surface area for bacteria to live, grow, and multiply.

What is the role of a Biofilter in an Aquaponics System?

Biofilters that are used in aquaponics systems are used to create a surface for bacteria to colonize and proliferate from. The bacteria inherent in the aquaponics nitrogen cycle are required to break down ammonia caused by fish waste, into nitrates. Nitrates are a bioavailable food for the plants in your aquaponics system

Filled with bio media that encourage bacterial growth, the role of biofilters in an aquaponics system is to engage in a two-step process.

  1. First, the Nitrosomonas bacteria that have formed on and around your biofilter transform the ammonia, found in excretions from fish, into nitrates, 
  2. Now that the first stage has occurred. Next Nitrobacter, another type of bacteria converts the nitrates into nitrates. These nitrates are now a bioavailable food source for your plants to live on

Biofilters also serve as physical barriers. Their surface area not only gives a home to the bacteria but also creates a physical barrier that slows down particles and allows for the nitrifying bacteria to do their job.

Oxidization is also a crucial part of the nitrogen cycle at play here. Due to this reason, biofilters need to be adequately aerated. Aquaponic farmers frequently insert air stones within the biofilter to ensure it is properly aerated. These air stones provide the necessary oxygen the bacteria need to carry out the nitrification process.

Types of Biofilters Used in an Aquaponics System

There are a variety of Biofilters that can be used in an Aquaponics System. Here we will talk about 3 of the most common

Moving Bed Filter

A type of filtration that is popular in Aquaponics is a system, known as a moving bed filter. This type of filtration unit is usually some type of container filled with submerged media, such as plastic bio-balls or K1-sized media.

The media contained in the filter bed moves continuously due to water flow and aeration that are driven by pumps. Despite all this movement in such a dynamic environment, the bacteria can colonize and start their work in the nitrogen cycle.

These bacteria break down harmful ammonia and nitrite compounds produced by fish waste into nitrate, which is less toxic to aquatic life.

As water flows through the moving bed filter, the bacteria attached to the media surface help in the biological filtration process, purifying the water and making it suitable for plants and fish in the aquaponics system.

The constant movement of the media prevents clogging and promotes efficient bacterial growth, ensuring a stable and healthy environment for both aquatic animals and plants.

Drip Filter

In aquaponics, a drip filter is a part that is used to filter and remove solid waste and particles from the water. An essential part of any aquaponics system as it works to help create and maintain healthy water quality and clarity.

Drips filters, generally consist of a container filled with filter media such as foam pads, bio-balls, or some other type of mechanical filtration materials.

Water from your aquaponic system is dripped or pumped through this bio-media filter setup, which allows it to trap solid particles suspended in the water.

As the water drips through these barriers, physical waste is also removed, resulting in cleaner water.

One of the downsides to this type of filtration setup in an aquaponics system is the added maintenance it requires. To ensure your system is filtering efficiently you will need to replace any worn or dirty filter media periodically.

Proper filtration is crucial in aquaponics because it helps prevent the buildup of harmful substances in your fish and plants.

Static Filter

The way a static filter works in aquaponics is by allowing water to flow through a physical barrier, such as a plastic or clay media, or even some mesh or a sponge. This method works to capture the solid particles present in the water.

Static filters are called “static” because they do not involve moving parts or require electricity to function. Relying on gravity and the bio media present to trap and process the solid waste makes static filters a popular choice in small-scale and home aquaponic systems

They rely on the force of gravity and the design of the filter media to trap solid waste. These filters are relatively simple and cost-effective, making them a popular choice in small-scale and home aquaponic systems.

Does my Aquaponics System Need a Biofilter?

Not all aquaponics systems need a stand-alone biofilter. The main reason to add in a biofilter is to create a surface area to collect and harbor bacteria. Some aquaponics systems have this as part of their inherent design.

Media bed systems generally won’t need an extra biofilter added to the setup as the media bed itself is the biofilter. As long as you are stocking your plants and fish to the correct ratio you won’t need any added surface area for bacteria growth.

Aquaponics Raft Bed and Nutrient film technique systems on the other hand, due to their lack of surface area, don’t have as much room for bacteria. This is why you will need a biofilter added to these types of systems.

Still Unsure? Please see this aquaponics filter compilation video below from one of our favourite Australians, Rob Bob!

What to consider when choosing a biofilter for Aquaponics

There are several things to consider when using biofilters for aquaponics. These aspects will help guarantee that the biofilter performs well and contribute to the aquaponics system’s overall performance.

Size and Capacity

The size and capacity of your aquaponics biofilter will be determined by how many fish and plants you will want to stock. More fish and plants will mean more biofiltration.

Media Size and Selection

Special attention must be given to the type of media used. This will go a long to prevent clogging and maintain optimum water flow. You will need to consider the size, surface area, weight, and durability when choosing a bio-media for your aquaponics system.

Click this link to see our favorite.

Water Flow and Oxygenation

Enough water flow guarantees equal water distribution throughout the biofilter and promotes effective filtration. Oxygenation is crucial to maintain aerobic conditions and promote the growth of beneficial bacteria. 

Nutrient Balance

It’s essential to keep the biomass of plants and fish in balance. The biofilter’s efficacy may be hampered by system overloading. Ensuring the biofilter can adequately handle the waste the fish create is crucial.

Upkeep and Inspection

To ensure the biofilter operates at its best, routine maintenance procedures like cleaning the biofilter media, checking water parameters, and inspecting equipment should be carried out regularly.

The pH and temperature

These factors can impact the activity of the bacteria in the biofilter. Their growth and effectiveness depend on monitoring and maintaining appropriate temperature and pH levels of aquaponics.

Design and Integration of Systems

The biofilter should be correctly incorporated into the aquaponics system design, considering elements like water flow, piping, and available space.


Your aquaponics system can be kept running smoothly and steadily with the help of a proper filtering system. While not usually necessary in media bed setup, additional bio filtration may need to be added to other systems to make up for their lack of surface area – crucial for the housing of bacteria

To maintain the long-term health of your aquaponics system, investing in a high-quality filtration system, and maintaining it properly is a wise course of action

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