As soon as you put fish in your tanks, they will start producing ammonia (in their wastes). Nitrosomonas bacteria in the air will populate the water surface, and start converting the toxic ammonia into nitrites. Nitrites are still toxic, but their presence will attract nitrobacter bacteria. These will colonize your system and convert the nitrites into nitrates, which are harmless to the fish and excellent fertilizes to the plants.

When this happens, you will be able to detect nitrates in your system, and the concentrations of both ammonia and nitrites will drop below 0.5ppm. This will signal that your system is now up and running! This will generally take about four to six weeks in total.

A method of starting up the aquaponics system which is becoming increasingly popular is the 'fishless' one, where you do not use the fish as the initial source of ammonia. Instead, you start up the system without any fish in the tank and add artificial ammonia. To do this, you should buy Cycling Kits, which will give you all the tools you need to start your system. Then, you add the fish once the system is up and running and the bacteria are thriving (i.e. when the levels of ammonia and nitrites drop to below 0.5ppm).

This method is safer, as there is no danger of having fish dying due to initial ammonia spikes. If you are using the 'fishless' method, you can also speed up the process by modifying the other parameters. One of the main ways to do this is to use higher temperatures (typically 77 to 86°F), as bacteria multiply more rapidly at these temperature ranges. You can also use a pH of about 7 to 8 to speed up bacterial growth and oxygenate the tank as much as possible, for example by using air stones and some kind of water jetting action. In addition, you can also buy bacterial colonies, which will definitely speed up the process. Alternatively, get some filter material or gravel from an established, disease-free aquarium as this will be rich in the bacterial colonies we want. You can also get some rocks and pebbles from a river or lake, but be careful of the risk of introducing disease and parasites.