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Nutrients & Bio-filters In Aquaponics. A Quick Guide!

Updated: Jul 12, 2021

All creatures, whether vegetables and fish, will never grow properly without an understanding of nutrients, bio-filters and how to use them in the aquaponic system.
The Aquaponic Cycle

All creatures, whether vegetables and fish, will never grow properly without an understanding of nutrients, bio-filters and how to use them in the aquaponic system.


The point of aquaponics is to create a closed-cycle system which doesn’t require you to supplement your plants with fertilisers. Water from the fish tank should be able to provide all the needed nutrients for your hydroponic crops.

In order to understand how aquaponic nutrient flow works, we need to look at the main chemical pillar of aquaponics - the nitrogen cycle.

Nitrogen (N) is a chemical element and a building block of all life forms; it is also a major food source for plants.

One of the major sources of bioavailable nitrogen in nature is the decay of animal waste and metabolites. In natural ecosystems that aquaponic systems are trying to mimic - nothing is wasted.

Animal waste (excrement) is largely made of ammonia (NH3). Other decaying organic matter such as residual food, and dead plants or animals, is also broken down to ammonia by the action of microorganism. By itself, ammonia is toxic and it is not so bioavailable to plants. That is where a special, naturally occurring group of nitrifying bacteria come into the picture. They belong to genera Nitrosomonas and Nitrobacter, and form colonies in the form of biofilm on the surface of inert materials in the water.

How are nutrients produced during nitrification process?

In aerobic conditions, first the ammonia-oxidising nitrifying bacteria convert the ammonia into nitrite compounds (NO2). Then, the nitrite-oxidising bacteria take over and convert them into nitrate compounds (NO3). Plants will then use nitrates with ease.

Also, if there is a need to boost the pH level of your water, a useful side-effect to that might be adding more nutrients. If you use calcium hydroxide and potassium hydroxide to raise pH to the desired neutral level (7.0), you will end up supplementing the water with calcium and potassium, which are the sometimes-deficient elements required for plant growth and good yields.

The whole process of nutrient optimisation - from nitrification to pH takes place within the system’s bio-filter.


Although the name sounds robust, bio-filters are quite simple setups - they consist of a vessel or a tank connected to air pumps, and a kind of substrate that provides as big as possible surface for the growth of nitrifying bacteria. More surface for formation of biofilm means more bacteria, which promises a more efficient nitrification process.

Good bio-filtration is the key pillar of chemical stability of your aquaponic system.

Even the medium is quite simple. Media commonly used in the bio-filters are sand, gravel, shells or specialised plastic media such as BioBalls.

Since nitrifying bacteria are aerobic, meaning that they require the presence of oxygen to live and grow, having additional aeration within the bio filter is also recommended.

How do bio-filters work:

Bio-filtration happens through three main steps.

  • The air pump gets the water out of the the fish tank and into the bio filter.

  • Water goes through the nitrification process in the filter.

  • Water robbed of unwanted chemicals, but still containing nutrients, is forwarded to plants.

Note that this is a general scheme for typical aquaponic setups, but know that steps may vary depending on the design. In some systems, water arrives to the tank via gravity. Other systems unify filtration with the hydroponic unit, using the hydroponic medium as a habitat for bacteria.

Types of bio-filters:

The four common types of bio-filters are:

  • Rotating biological contractors

  • Expandable media filters

  • Fluidised bed filters

  • Packed tower, or trickle, filters

You can buy or order a bio-filter, or make one yourself. Homemade bio-filters are known to be of a superior quality to that of some commercial submerged pond filters.


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