Aquaponics Filtration Systems

Getting your aquaponics system just right takes time. However, it is worth making the effort to get your aquaponics filtration system right first. Your reward will be a good quality yield of healthy crops with minimal intervention from you.

Setting up an aquaponics filtration system is actually fairly straightforward. Unfortunately if you’re not aware of the filtration issues; then you’ll quickly discover that your growbed will get clogged. This is because the waste particles created by fish are generally small but solid. Without the right help, the flow of water is interrupted and the plants cannot get the nutrition they need, creating an anaerobic zone.

Why Aquaponics Filter Systems?

Bacteria in your water will convert the ammonia produced by your fish into nitrates which are needed by the plants to ensure healthy growth. Check: What is aquaponics?

This is a natural process that occurs in nature as well as in your aquaponics system. The bacteria help to keep your fish healthy by filtering the water and removing toxic elements.

But, not all particles in the system are dissolved. Larger particles of waste are left over and will be pumped to your grow beds, floating rafts or NFT system. These are the dangers of each system:

  • Grow beds: It will clog up the growbed creating aerobic zones where the bacteria can live in, thus lowering the surface area of your system.
  • DWC (rafts): Solids will create a sludge at the bottom of the trays and create gasses and aerobic zones for bacteria. Solids will also be lifted to the roots because of the aeration and will stick to them creating brown roots.
  • NFT: particles will get trapped in the roots and will eventually block the water flow.

They can then block the flow of water; preventing the plants from getting the nutrients they need and depriving the fish of clean water.

Fortunately, this can be prevented by filtering the water when it leaves the fish tank before it enters the growbeds, DWC or NFT channels.

Most Common Filtration Systems

Your fish need clean water in order to remain healthy; this is why it is advisable to filter the water in their part of the system. You can choose between these filters:

Swirl Filter (Vortex)

These are filters that are shaped like small barrels. Inside the barrel is a basket.  At the base of your basket you can add your choice of filtering material.

swirl or vortex filter

You then allow the water through from your fish tank. This comes in halfway down the barrel wall. The fore it arrives with creates a swirl inside the barrel. As the swirl slows the water rises and can go out of the tank and into the plant bed through a pipe at the top of the barrel.

The key to this approach working is that the barrel is large enough to create a good swirl. The high level of flow allows the larger particles to sink to the bottom of the basket and stay there; preventing the hard particles from blocking up the system.

Raft Filters

This type of filter looks a little like a raft floating in a large tank.

The large tank of water is split into several sections. Water from the fish tank flows in at the top of the first chamber; where you’ll need to place three types of filter.

raft filter for aquaponics

It is normal to use large foam pieces as the filters; these will trap the larger waste particles and even dirt particles; allowing clean water to move onto the next chamber. The majority of the waste simply floats to the bottom of the tank.

The water only moves between chambers when it overflows. It is a good idea to use two foam pieces to create each wall; this will ensure that you can remove one for cleaning without affecting the next one.

Once the water has been through all three chambers it is clean enough to be pumped back into the plant tank.

Again, the water must be removed from the top. Entry and exit at the top are important to ensure the particles which have settled are not dragged into the plant tank.

It is important to note that the raft system is one of the best you can install but it requires a fairly large tank. You will also need to shut the water off periodically in order to remove the sludge which starts to build up at the bottom of the tank.

The Mechanical Filter

It is possible to adapt the above systems to fit your specific needs or even to purchase a pump that is designed to filter water and remove certain materials. However, these are generally very expensive and may not produce any better results than the filters mentioned above. After all, a mechanical filter simple applies the same technology as the swirl filter; but with power behind it.

One way of achieving this is to get a pair of tights and cut several sections out of them. These can then be secure over the inlet and outlet pipes of your filter. The tights will be an extra filter, preventing the larger particles from getting into your small pipework.

You’ll need to empty the tights periodically to ensure they don’t become the source of any clogs.


Solid waste particles are heavier than water and will settle given the opportunity. This makes it easier to remove them and protect your system. However, it is worth noting that you can reduce or even eliminate the number of particles in your system just by following a few simple rules:

  • Don’t overfeed your fish; this will prevent fish food from clogging your pipes.
  • Don’t use the cheap fish food; it won’t help your fish and it will increase the amount of waste.
  • Don’t have too many fish! Always calculate fish numbers based on the size of the fish when they are adults. Too many fish equals more waste than the plants or your system can handle.

If you are not sure about the quality of your fish food or the filters simply take a look at the roots of your plants. If they are slimy and grey or brown then there is too much debris in the tank; you need to reduce and change the fish food. Getting this one factor right should eliminate the need to add any filtration system unless you’re planning to go into large scale production.

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