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Water Filtration In Aquaponic Systems

Aquaponic systems are closed water circulating systems and this brings a lot of challenges when it comes to water filtration.

For aquaponic beginners water filtration can sometimes be a nightmare.

After successful start of aquaponic system usually everything looks fine for a short period of time. But, after just a week or two solid particles that are produced by fish start to make quite a problem.

Nozzles start to clog and fish waste deposits start to create serious challenges that make a lot of people give up aquaponics.

Luckily I have not given up but I’ve found a solution for all the water filtration problems and would love to share my experience and some practical solutions with you.

Mechanical water filtration in aquaponic system

Chemical filtration in aquaponic systems is very important. It happens completely naturally by microorganisms that convert ammonia produced by fish. By converting ammonia bacteria is not only saving your fish but it also produces natural nutrients for your plants.

When plants absorb nutrients they chemically filter the water and return aerated water to your fish. If we would exclude plants from aquaponic system a lot of toxic elements would build up in your aquaponic system and this would kill your fish.

Chemical filtration by microorganisms and plants happens the same way as in nature and as far as chemical process is concerned. If you’ve build your aquaponic system the right way, you don’t have to worry about this.

But, on the other hand solid particles that are residuals of fish food and fish waste, that has not dissolved, can create serious problems in your aquaponic system. They can clog your piping, nozzles and plant roots and this can create quite a headache if you are not prepared and don’t have solution for this.

When water is transferred from your fish tank to the sump tank it needs to be filtered the right way.

When you filter the water at this point you can practically prevent all the problems down the line, that might be caused by solid particles in the water.

Related article:  How To Create Great Aquaculture Environment

Water filter types

Mechanical water filtration of fish waste and residuals of fish food is usually done by hand made filters. These filters help with maintaining water clarity that the fish can thrive in.

The health of the fish deteriorates whenever the water is murky and full of fish waste and food debris. For Deep Water Culture (DWC) systems mechanical filtration is necessary, in order to prevent plant roots from getting clogged since this is detrimental for the health and growth of the plants.

There are different ideas and solutions for this water filtration.

SWIRL water filters

They work by slowing the water whirlpool in a barrel (that presents your swirl filter). When the water slows down big particles that are heavier than water fall on the bottom of the barrel. You’ll then distribute the water to the rest of your aquaponic system from the top of the barrel. Take a look at the picture.

Swirl water filter

Please note that for swirl filter to work the barrel needs to be big. If you would  use small container the filter would not work. Large quantity of water with high water flow would create problems. Particles would not end up on the bottom but would continue to flow into the system, to your sump tank or growing beds.

With this type of filtering the most important thing is to have a calm water surface. The water is directed from a fish tank via a pipe that is shaped so that the waste water that comes in is forced to swirl on the bottom. But, to get calm water surface that is circulating slowly and pushing solid particles to the bottom you need to have large barrel.

This is practically the biggest downside of swirl filters but it’s not the only flaw. Swirl filter cannot filter all the particles so it’s used as the “first line of defence”.

After some time the waste in swirl filter starts to collect on the bottom. You will need to clean it and to do this, all you need to do is take it out and wash it. One thing you need to be aware of is that filter will have good bacteria living in it that you’ll want to keep. So the filter should be washed without any detergent in cold water.

Raft water filter

Raft water filter is very good at filtering solid particles. The main reason this kind of filters is one of the best solutions is in the fact that it’s multilayer filter.

Raft water filter

Water is entering the raft that has couple of chambers. In the first chamber the biggest particles are filtered and this is done by three media filters. After this the water overflows the barrier that collects milk dust. These fine particles are left behind on the bottom of the raft and after that the water exits filter and moves on to the next system element (sump tank or grow beds).

The main disadvantages of this filtering system is that it is quite expensive to build and it requires a lot of space but this is surely one of the best filters in aquaponics.

My solution and upgraded swirl filter

I have tried both, swirl filter as well as raft filter for my aquaponic system. Because I use dutch bucket system for growing tomato and vertical towers for growing strawberries I had many problems with piping and nozzles clogging with both filters.

Smallest particles always managed to get into the system and screw my nozzles and small pipes I used for vertical towers and buckets. They deposit by time and create real headache.

What solved all my problems is one very simple and ridiculously cheap upgrade to swirl filter.

All you need to do is to look at the facts and to identify the problem and dependent factors.

The problem, that require mechanical filtration, are residual particles from with waste and fish food that did not get to grow media where it will be dissolved by worms and bacteria.

These particles are flying through our system and making all sorts of different problems. Especially if we use small nozzles for watering dutch buckets and vertical towers.

Seemingly very benign thing but it can create a lot of problems. It’s enough to have one nozzle clogged without you noticing and there you have a problem. Now imagine if you have hundreds or thousands of dutch buckets. It makes it impossible to track and control.

The best mechanical water filtration would be the one that separate all solid particles and is cheap.

With this goal I made a small upgrade to swirl filter that makes the best mechanical water filtration.

All you need to do is to add synthetic woman tights socks on the inline into swirl filter. If possible add one also on drainage pipes that take to water to sump tanks. 

Swirl filter upgrade

I had amazing results with this small upgrade. For two seasons I did not have any problems with nozzles. Until I did this I really had huge problems although I tried many different filtering techniques.

The benefits of this small upgrade are:

  • it’s extremely cheap
  • you can easily wash it
  • it collects even smallest solid particles
  • you can have really high water flow


I’m happy to share my experience and I hope this can help you solve filtering problems in your aquaponic system.

If you have any ideas or suggestions feel free to leave a comment or write me an email.
And off course, if you find this article useful please share it with you friends and other aquaponic enthusiasts.


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