Skip to Content

Aquaponics Biofilter: What is It and How does It Work?

Spread the Word!

In aquaponics, a symbiotic environment is created between plants and aquatic animals. This is made possible by the bacteria living within the aquaponic system, mainly the biofilter.

The biofilter is a component of an aquaponics system that contains bio media which increases the surface area for beneficial bacteria to thrive. The bacteria attached to the bio media convert ammonia into nitrates or nutrients for plants to grow.

Aquaponics systems require little intervention from you since the fishes and the bacteria does most of the work.

Although the biofilter facilitates the conversion of toxic ammonia into nutrients. There are factors such as media size, media type, and biofilter design to consider to ensure that the biofilter is functioning properly.

What is an Aquaponic Biofilter?


An aquaponic biofilter houses beneficial bacteria by providing the right environment for them to thrive. The biomedia it contains provides a large surface area for bacteria to live and covert the fish waste into plant nutrients in an aquaponic system.

The biofilter has a big part to play in the design, layout, and operation of a successful aquaponic system and is usually placed after the mechanical filter.

This is because the mechanical filter firstly removes the heavier fish waste preventing the biofilter from being overloaded and clogged.

The demand of the system is based on the number of fish in the system and the waste they produce. This in turn, determines the actual sizing of the biofilter which we will discuss further on.

Biofilters are essentially made by filling a container with bio media, which are designed to increase the surface area for the bacteria to live.

The biofilter houses the beneficial bacteria and is designed such that it does just that.

Some people may say it sometimes is not necessary to have a biofilter. But this is not true.

Although the bacteria can live anywhere in the aquaponics system, they eventually will not be able to handle the load as the system and the fishes age.

My Aquaponic setup

Build a successful system with these affordable equipment from amazon, that I’ve tried & tested on my setup.

Click on the links to see them

Best water pump
Best Water Pump
Best air pump
Best Air Pump
Best air stone
Best Air Stones
GROWNEER 25 Packs 4 Inch Garden Slotted netcups
Plant Net cups
Bio Balls
Bio Filter Medium
API Freshwater Master Test KIT 800-Test
Water Test Kit
The Aquaponic Equipment Essentials that I use in my system.

What is Bio media?

Biomedia in aquaponics is any medium that creates a large surface area for nitrifying bacteria to attach themselves onto.

The bio media when placed in a container with proper aeration creates what’s known as the biofilter and creates the perfect environment for nitrifying bacteria to convert ammonia into nitrates.

Bio media can be DIY’ed by using any material with a large surface area or it can be bought from any aquaponics store. We will discuss the different types of bio media further in the article.

How does a Biofilter Work?

The biofilter works by housing bacteria that convert ammonia from the fish waste into nitrates for plants to grow. This is done in a two-step process called Nitrification.

Firstly, the Nitrosomonas bacteria convert the ammonia to Nitrites after which the Nitrites are then further converted to Nitrates by the Nitrobacter bacteria.

The environment inside the biofilter should be bacteria friendly. Happy bacteria makes happy plant and happy fishes and for this reason, it is important that the environment that the bacteria lives is kept within certain limits.

The conversion of ammonia to nitrate can only be carried out in a environment where the water pH is at around the 7.0 to 7.5 range. The nitrification process is at its peak at this range.

When the Nitrification process occurs, however, it lowers the pH of the circulating water in the aquaponics system, thereby requiring you to implement some type of pH control to the water to keep it at around 7.0

With a pH range below 7.0 the nitrification process tends to slow down.
What does this mean for the system?

  • Less ammonia is converted to nitrates
  • Less nutrients are available for the plants to grow
  • A build up of ammonia can cause fishes to die.

Nitrification is also an oxidation process whereby the ammonia is sequentially oxidized into Nitrites and Nitrates.

For this reason, the biofilter should be properly aerated.

To ensure the biofilter is properly aerated, aquaponic farmers often place air stones inside the biofilter providing the necessary oxygen required by the bacteria to carry out the nitrification process.

See our complete guide on aquaponics and what you need to know to run a successful system.

Types of Biofilter for Aquaponics

Biofilters for Aquaponics come in many designs and all accomplish the same task of increasing the aquaponics surface area for bacteria to thrive in a well-oxygenated environment.

The three most popular biofilter aquaponics systems use are –

  1. Moving bed filter
  2. Static filter
  3. Drip filter
  1. Moving bed filters normally incorporate K1 media which is a small finned cylindrical shape medium. This is placed in the biofilter with an air stone at the bottom.

    The biofilter is designed such that the air stone is placed at the bottom of the filter causing bubbles to move upwards, churning the K1 media to be in constant erratic motion motion.

    Hence the name Moving Bed Filter. Another name for this is Moving Bed Bio Reactor (MBBR) which signifies a biological reaction occurring in a the biofilter.
Moving Bed Filter
Moving bed Biofilter

2. Static Filter – These biofilters are designed like flat trays in which the filter media sits. These trays are submersed into the water and are located upstream of the plants.

3. Drip filter In this type of biofilter the trays containing the bio-media are stacked on top of each other with the water being applied from the top. The water is then allowed to drip through the beds and then out towards the plants.

How to Design a Biofilter for Aquaponics?

The following factors are used to determine how the biofilter is designed

  1. Direction of water flow
  2. Adequate aeration
  3. Surface area based on the amount of fish

1. A biofilter should be designed such that the water enters at one end of the filter and then leaves at the other.

This should be done to ensure the maximum resident time of the water inside the biofilter. By spending more time inside the filter there would be more ammonia to nitrate conversion taking place.

2. Also the air stone should be placed at the bottom of the filter so that the air bubbles would move up and through the bio media, aerating and properly oxygenating the water.

3. More surface area means more bacteria. So increasing the surface area by using the correct bio-media is essential for the biofilter to function properly.

Types of Bio Media used in Aquaponics

The purpose of bio media is to create surface areas for bacteria to live.

Bacteria in an aquaponic system live everywhere within the system, and although this is true, having a biofilter with bio media is very important as it substantially creates a very large surface area for a thriving bacteria habitat.

Some bio-media includes

  1. AQUANEAT Aquarium 1″ Bio Balls
  2. Fluval BioMax Bio Rings
  3. Seachem Matrix Bio Media
  4. K1- hygger High Surface Area Floating Moving Filter Bio Media
  5. DIY – bottle caps or old nylon fish nets.

When a Biofilter is Not Required

A biofilter is not required in a system where you have media beds. This is because the media itself acts as a biofilter because it creates a large enough surface area for the bacteria to live.

Although this is true for this type of system, you would still have to provide proper aeration and pH control to create the right environment for the bacteria to thrive.

How Long does a Biofilter take to work?

Once you’ve started circulation in your aquaponic system you may have to get a starter solution. A starter solution is basically water from an already established system that contains bacteria. This drastically speeds up the process of cycling.

Cycling refers to the colonization of nitrifying bacteria in an aquaponic system to establish the nitrogen cycle. The bacteria necessary for colonization will begin to show up when ammonia is present. This may take a few months. But by adding the starter solution the time will be reduced.

Once circulation is started, maintaining the right water pH and temperature is very important to ensure that the bacteria colonize the biofilter.

The fish in your system will also play a vital role in this process by providing food for the bacteria. It is, however, not recommended to place too much fish in the system when you are now starting out.

Doing this would lead to an overdose of ammonia which the aquaponic system will not be able to handle.

How do you Make Bio filter Media?

If you want to go down the DIY route, you will just have to choose a medium that creates a large enough surface area.

I have found the used bottle caps work well as a biofilter media. The only downside is locating all the caps.

Old fishnets are another alternative and are very effective as a bio-media substrate. So if you have some at your disposal you can definitely use those.

Spread the Word!

Free Plant Care & Gardening Guides