In a newly set-up Aquaponics system, the bacteria will need some time to colonize the medium. This is why a process called 'cycling' is used. There are two methods of cycling your system - using fish right from the start or putting the fish in only when the bacteria have established themselves. The first method takes 4 to 6 weeks, while the latter is quicker and can be done in about 10 days. Cycling without fish (using ammonia) is also safer.

An important aspect in the system that is needed to ensure a steady supply of plant nutrients is pH. If this is not optimal, an accumulation of toxic materials will build up, and nutrient generation by the bacteria will be halted. In addition, pH outside the range will make it harder for the plant roots to take up nutrients and can harm the fish. Try to keep your pH at around 6.7 to 7. If your pH is outside the range, get commercial pH regulators to increase or decrease the pH. Alternatively use vinegar to lower the pH and calcium carbonate or baking soda to increase the pH.

Although some Aquaponics farmers use nutrient supplements, in a properly managed system supplements are never required. In addition, if you use supplements you need to be very careful, as some can harm the fish. As long as you keep the pH at 6.7 to 7, and the water well oxygenated, the bacteria will provide more than enough nutrients for your plants.

The only substance that it may be beneficial to add is salt. Salt is often added to Aquaponics systems at 1 to 2 ppt (parts per thousand; meaning 1 kilo to 1000 liters of water). Adding salt increases the resistance of the fish to disease and infections, because it has a positive effect on the mucus layer of the fish. If you decide to add salt, it is important to keep the concentration below 2ppt and to use pure sea salt - not table salt.