Getting Aquaponics system up and running

Getting your system up and running


OK, if you’re reading this page you’re committed to building an Aquaponics System and you don’t want to make the same mistakes we made at New Wave Aquaponics. I cannot stress how important this process is. I got the brilliant idea to start off with adult fish in my stock fish tank and I paid dearly for this mistake, you want to fallow the startup process exactly as stated and you will have success.


Starting up your aquaponics system involves getting beneficial bacteria established in the grow bed. This process is known as cycling and is vital to the success of your system. This article covers cycling aquaponics systems in detail.

Toxic substances are produced from fish waste and respiration, and these have to be broken down into a form that can be absorbed and used by the plants. This is carried out by beneficial bacteria that colonize the grow beds.

The process by which fish waste is broken down and used by the plants is known as the nitrogen cycle, hence the term “cycling”. Ammonia from fish waste and respiration is converted into nitrite by bacteria known as nitrosamines. The nitrites are then converted into nitrate by bacteria known as nitrobacters. The nitrate is then absorbed by the plants. Essentially, bacteria converts fish waste into food for the plants, at the same time keeping the fish safe.

However, in a new system this beneficial bacterium has to build up and establish itself. In order to do this ammonia is added to the system, providing a food source for the nitrosamine bacteria. During cycling, aquaponics system grow beds are colonized by bacteria. These bacteria are built up to such a level that they can cope with the levels of ammonia produced by the fish.



As the nitrosamine bacteria converts ammonia to nitrite, it provides a food source for the nitrobacteria. Again, during the cycling process, these bacteria are built up to such a level that they can cope with the levels of nitrite produced by the nitro soma bacteria.

When the nitrobacteria bacteria convert nitrite to nitrate, it provides a food source for the plants.



There are two methods of cycling aquaponics systems, with or without fish. If fish are used, they are the source of ammonia. With fishless cycling you provide the ammonia source, thereby taking the fish out of the equation.

Fishless Cycling should be used for a number of reasons. First and foremost is the well-being of the fish. Cycling aquaponics systems with fish is stressful for the fish at best. High levels of ammonia cause burns, especially to the delicate gill structures. Even though the fish may survive, their future health will be compromised and their lifespan will be shortened.

Also, fishless cycling is quicker and involves less work. Because you can have a much higher concentration of ammonia than you could with fish, the process is speeded up. Fishless cycling takes from 10 days to 3 weeks, as opposed to 4-6 weeks if you use fish. Cycling aquaponics systems with fish also means lots of water changes. Once a system has cycled you can fully stock the fish tank, whereas if you use fish you have to stock it gradually. Also, with fishless cycling you can control the concentration of ammonia so it is at an optimum level.



There are two recommended sources of ammonia – liquid ammonia and ammonium chloride.



Ammonium Chloride:

Ammonium chloride is pure ammonia in crystalline form. You can get this from aquarium shops, sold specifically for cycling. If you buy it from another source, make sure it is food grade to be on the safe side.



Liquid Ammonia:

Liquid ammonia is sold as a cleaning product and is safe as long as you use “pure” ammonia. Pure ammonia is actually ammonia diluted with water, usually between 5 and 10%. If it has anything else added then avoids it. If you shake the bottle and it foams it will have additional ingredients, such as surfactants, perfumes etc. You can get this from a hardware store, or failing that, try online.




In addition to a source of ammonia you will need to monitor the levels of ammonia, nitrite and nitrate. You can do this with simple, inexpensive test kits sold for aquariums etc. the Hagen Nutrafin range of test kits.



Fishless Cycling Step By Step

  • Gradually add ammonia to the tank until you get a level of around 2 ppm
  • Test daily until there is no trace of ammonia (this may take several days)
  • Add more ammonia to bring it back up to around 2ppm
  • Repeat this process until you get no trace of ammonia 8-12 hours after adding it to the tank
  • Test for nitrite
  • If there is no trace of nitrite, go to the next step. If not, repeat the previous step 3-4 times then test again for nitrite
  • Do very large water change (about 90%), making sure the water you add is around the same temperature as the water in the tank
  • Add your fish

Speeding Up the Cycling Process

When cycling aquaponics systems, the process can be speeded up by adding bacteria to the system, rather than waiting for it to show up on its own. Heating the water to the optimum temperature will speed things up further.

Bacteria can be obtained from the following sources:

  • Media from an existing aquaponics system
  • Filter media from an established, disease-free aquarium or pond
  • Squeezing’s from a filter sponge, from an established, disease-free aquarium or pond
  • Gravel from an established, disease-free aquarium
  • Commercial bacteria product etc. Cycle – the jury is still out on the effectiveness of these products


The best temperature range for cycling aquaponics systems is between 86-95°F (30-35°C). This is the optimal range for the nitrifying bacteria. You can use a suitably rated aquarium heater, or multiple heaters, to raise the temperature during cycling. You will need to monitor the temperature, and the easiest way is to use a floating pond thermometer. Once cycling is complete allow the temperature to drop to the right level, then do a water change as mentioned previously.





The flood and drain system is the easiest to understand and put together. It is also cheaper to buy or build this type of system. Therefore, it is the most suitable type for beginners to aquaponics. How to build one will be covered shortly, but first an overview.




Flood and Drain System Overview

The main components of a flood and drain system are a grow bed and a fish tank. The grow bed is filled with expanded clay balls or gravel and is situated above, or at a higher level than, the fish tank.

Water from the fish tank is pumped into the grow beds then allowed to drain back into the fish tank. Flooding and draining is controlled by an auto-siphon, which is a simple device unique to aquaponics. Alternatively, a timer can be used to control the pump. This alternate flooding and draining is repeated continuously.