The nitrogen cycle in aquaponics

The nitrogen cycle refers to the chain of transformations that nitrogen-rich waste undergoes in the water. Specifically, fish release ammonia and ammonium (NH₃/NH₄⁺) into the water through their excrement and respiration. However, these two compounds are highly toxic to aquatic organisms. Without intervention, they would accumulate and endanger your fish within hours or days, depending on population density.

Fortunately, in a balanced aquaponics system, ammonia and ammonium are gradually converted into less harmful substances through the action of microorganisms. This nitrification cycle results in the formation of nitrates, which are well tolerated by fish and serve as fertilizer for plants.

During this cycle, nitrogen passes through three main chemical forms. Ammonia and ammonium, first, come from fish waste (urine, feces, respiration). Ammonium is less toxic, but both are dangerous at high concentrations. Specific bacteria then oxidize these compounds into nitrites, a second form that is equally toxic to fish.

Finally, other bacteria convert nitrites into nitrates. Nitrates are the end product of the cycle : they are not harmful to fish and become an essential source of nutrients for plants.

This nitrification process in the aquaponic system is carried out by nitrifying bacteria naturally present in the water. In aquaponics, there are mainly two genera of useful bacteria : Nitrosomonas and Nitrobacter .

Nitrosomonas oxidize ammonia and ammonium into nitrites, while Nitrobacter converts nitrites into nitrates. They colonize the substrate (culture bed media, bioballs, pozzolan, etc.) and continuously treat the water circulating there.

It is important to understand that nitrifying bacteria need favorable conditions to thrive : dissolved oxygen (since they work by oxidation), a suitable pH (around neutral) and time to establish themselves.

This nitrification (nitrogen) cycle, carried out by beneficial bacteria, is essential for converting fish waste into nutrients that can be used by plants. If you introduce fish too quickly into a new system, ammonia and ammonium can build up to toxic levels due to a lack of sufficient bacteria, leading to fish stress or mortality.

Wait a few weeks for the bacteria colonies to develop. Monitor nitrogen parameters with tests during this break in phase. Only introduce fish once nitrites decrease and nitrates begin to appear, a sign that the cycle is operational.

Even after the initial cycling, an imbalance in the nitrogen cycle can occur and affect your aquaponic ecosystem. It is important to recognise the symptoms of a poorly established or failing cycle. On the fish side, watch for signs of stress : fish gasping rapidly at the surface, becoming lethargic or losing their appetite — these can indicate a nitrite or ammonia spike. On the plant side, yellowing foliage or stunted growth is often a sign of insufficient nitrate (nitrogen deficiency).

The number one rule is to test your water regularly. Equip yourself with a comprehensive aquarium water test kit, including ammonia, nitrite and nitrate tests. It is the only way to measure these invisible parameters accurately.

Ideally, test weekly and record the results. You should always achieve a maximum of 1 mg/L of NH₃/NH₄⁺, 2 mg/L of NO₂⁻, and a certain level of NO₃⁻ corresponding to your plants' consumption. If ammonia or nitrites rise, don't wait: reduce fish feeding (overfeeding is a common cause of ammonia spikes), temporarily add extra aeration, and do a partial water change if necessary to dilute toxins. Also, remember to maintain the biofilter without sterilizing it; never rinse the filter media with chlorinated tap water, for example, as this will kill your precious bacteria.

Finally, when launching a new system or introducing new fish, take precautions to avoid overloading the nascent cycle. Similarly, you can "pre-cycle" a system by adding a source of ammonia (such as a pond bacteria activator) before adding the fish, which allows good bacteria to establish themselves without risking the animals' lives.