The three main forms of filtration are mechanical, biological and chemical.



Mechanical filtration is the removal of visible particles in the water. These particles are not harmful to fish, but can use oxygen as well as clog pipes and other filter media and grow-beds. Media-based beds such as expanded clay will add act as mechanical filtration for your system. There are also vast arrays of mechanical filters available to filter out various size particles of suspended matter, which in the most part is fish faeces and uneaten food. Mechanical removal of suspended solids is the first step to filtration and includes various grades of coarse, medium or fine to trap different sized particles. The choice of mechanisms include:

Screen filters

Drum filters

Protein skimmers. Foam fractionation

Settlement tanks

Sand filtration

Swirl/Whorl filtration

Grower’s tip: leafy greens will thrive with increased nitrate levels, so cleaning the mechanical filters less frequently will help boost them, similarly for fruiting plants, cleaning your filter frequently will help decrease nitrate levels.



Biological filtration is the most important filtration within an aquarium. This is where the Nitrogen Cycle comes into practice and bacteria breakdown organic pollutants.

Firstly, the fish waste which is mainly ammonia gets converted  into nitrites by thousands of bacteria including nitrosomonas bacteria and then into nitrates by thousands more including nitrobacter bacteria, the time it takes for this process to establish itself is around six weeks and called “Cycling”. There are thousands of other bacterial colonies that establish over time producing other nutrients but it’s the nitrogen cycle, which we pay particular attention to and monitor on a regular basis with a simple chemical test kit. Read our section on Water Chemistry for more information.

Sintered glass has a high surface area for bacteria as do expanded clay pebbles, ceramics and foam.

There are also a number of things you can use from the recycling such as magazine strapping which is often polypropelene (used to hold a brace of magazines for delivery) to increase surface are for bacteria to colonise




Chemical filtration is not usually recommended in aquaponics as it alters the water’s properties by removing one or more substances, e.g. heavy metals. It is certainly not necessary for everyday use, but occasionally useful for emergencies and problems which need quick solutions for example making tap water safe. Chemical filtration can upset the balance of the aquarium e.g adding activated carbon can remove pollutants such ammonia, metals and unwanted chemicals, however it also removes nutrients needed for plant growth.


Chemical treatment of water is also the reason tap water cannot be added to aquariums, because the levels of Chlorine, and more importantly Chloramine in water supplies can seriously harm or even kill the aquaculture. (This probably means we should filter it before drinking too).



Filters come in many forms, some are used in the aquarium whilst others are external, some have moving bio-beads in turbulent water while others gently drip water from layer to layer of stable media.



A pump inside the tank draws water through filter media.


Works in the same way as internal, but allows for greater sizes of filter/filter media.


Work by drawing water through the substrate which works as both a mechanical and biological filter. Not so long ago most home aquariums worked on the basis of an under-gravel biofilter prior to the vast array of filtration products now available and under-gravel filters were used less and less.


A natural way to include extra filtration in your system is to increase your biodiversity with freshwater filter feeders. Animals such as crayfish or freshwater shrimp will act as mini bio-filters as they feed on microorganisms in the water.


Cleaning your filter media

Using a bucket of water from your aquaponics system, rinse clogged filter media in it to remove solid waste. Use this dirty water to feed container plants outside of the aquaponics system – they will love the nutrient rich water! When cleaning the filters, you do not want to destroy the colonised bacteria, so never use tap water to wash filter media.



Sterilisation “filters” such as ultra violet light or ozone treatments are used to destroy pathogens, parasites and diseases that could otherwise harm your fish, they also destroy algae spores thus keeping them under control. There is evidence to suggest using UV filters long term could reduce certain mineral content in the water.




These are not as complicated as they sound, simply put it’s a water filled container with and air-stone in the bottom providing large quantities of oxygen to maintain a high dissolved oxygen content and off gas others such as carbon dioxide. These are not always necessary.



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