When you start aquaponics there is generally a 6 month period of time where the ecosystem is building up. After this period, the bacteria and other fungus reach a good diversity and density. The nutrients are highly available for the plants and the productivity is very high. Even after this point, the growbed is continuously building up with organic matters. This accumulation is composed of different particles: dead roots, fish poo, bacteria biofilm… With time those particles can clog and form a dense and compact “Cake” almost waterproof. This phenomenon will cause the following issues:

Nitrate increase

If your system is well designed and you respect the maximum fish biomass capacity of your system (Maximum 1kg of fish per 50Litres of media, watch this video for more information: https://youtu.be/7kjkQcsrJVk ) the quantity of bacteria is enough to transform the ammonia in nitrite and the nitrite in nitrate. The large quantity of nitrate released into the water is sometimes higher than the plant needs. In this case the nitrate will continuously increase into your water and you will have to continuously renew the water to keep them down. Cleaning the growbed and reducing the quantity of organic matters will significantly the quantity of nitrate produced and therefore decrease the quantity of water change necessary.


Poor water flow,

In aquaponics the whole ecosystem is relying on the capacity of the bacteria to transform the fish poo into plants fertilizer. Those specific bacteria are what we call “aerobic” which means that they need oxygen to live. If the growbed media is clog with organic matters, the water can’t circulate properly and therefore some are of the growbed will turn “anaerobic” which means without oxygen. This situation can be detected if you see some constant water pools near your water inlet. If nothing is done the good “aerobic” bacteria will die and leave the room to other anaerobic bacteria responsible for fermentation. The setup will then smell very bad and the ammonia level increase until the fish die.

Rotten roots

If the system is clog by organic matters, the media will become sealed and the roots of the vegetables will not be able to breathe properly. In this case you will see the plants growth slowing down until a point where the plants will die. In order to avoid this problem we must clean the growbed before the media becomes clog.

How to detect a clog media

When you dig into your growbed, the media should fall down as if you are digging into a sand bed. Each particle of the growbed must be independent and not clog to others. If you see a “cake texture” when you dig into the growbed, this is a sign of clogging.

When is a good time to clean the growbed?

It is generally easy to see a growbed media stating to clog. The best time of the year to clean a media growbed is winter. By cleaning your growbed in winter you avoid to disturb your plants during their best growth time.

How to clean the growbed?

In order to clean the growbed it is important to plan the operation. You must not feed your fish the day before and during the whole process. The D day, turn the water pump off, plug a pipe at the end of your bell siphon going directly into your classic growbed. Here we will remove a significant quantity of organic matters that we will use as a fertiliser in our classic garden. If your garden is mulched, you can push the mulch away and cover it back at the end of the process so that the “mud” will not be visible.

The second step is to remove all your plants one by one and place them in a safe place in a shady area. The roots must never be exposed to the sun.

The third step is to move the media in order to release the organic matters trapped between the rocks. You will add a water pipe in your growbed and turn the tap on. There are different techniques and options depending on the equipment you have available:

Air blowing technique

If you have a compressor or strong air blower, you can fill the growbed with water and blow some air in the media in order to move all the media particles and release the organic matters trapped in between.

Air + water technique

You can also associate your air hose with the water hose (tap them together). It will be the best tool for cleaning large growbeds.


If you don’t have a compressor, you can simply use a shovel and move the media to mechanically dissociate all particles. I strongly recommend to remove 30% of the media in buckets on the side. It will create some space in the growbed and help you to move the media more easily.

When you operate this step you can remove the bell of the bell siphon and leave the water over flow through the stand-up pipe. The water going into your garden will be completely black and full of nutrients for your plants J

Once the all media particles are free, you can continue moving them with full running water until the water turns from black to brown. The longer you clean the growbed and the clearer the water going out will be.

Don’t expect to see clear water going out or you will lose too much water. The idea here is to remove 80% of the particles, not to remove everything.

Once done you can put all the media back in place and replant the plants in the cleaned growbed. Leave the coming water on and check the water colour of the water going out of the growbed (into your classic garden). Leave the tap on until the water becomes transparent. Once the water is transparent you can put the bel siphon back in place and flush the whole growbed. Once done you can unplug the pipe going to the garden from the bell siphon evacuation and place your system as in original position.

Now you can turn the water pump on and the system is running as normal. Check the quality of the water going back to the fish tank. It will be slightly brown but shouldn’t be black.

After few hours test the water parameters. They may be slightly high. If it’s the case renew part of the water. Keep an eye on your fish and make sure the fish tank is well aerated. After few hours the water should start to clear again.

Congratulations! Your growbed is cleaned and your system ready to go for few more years before the next clean up 🙂

Welcome here! If you are new, you will probably be interested to discover Jonathan’s six steps to build and manage an Aquaponics system. Click here to access for free! Thanks and good reading 🙂