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The Nitrogen Cycle

Nitrates, nitrites, ammonia: where do they come from, and why are they dirtying up your fish tank? Various forms of nitrogen are the by-products of food consumption and digestion in all terrestrial and aquatic animals. In a natural environment, waste products are diluted and recycled continuously by a variety of processes. In the aquarium, waste is produced as food is added, but remains concentrated in the tank until it can be removed. The cycle is as follows:

Food -> Ammonia -> Nitrite -> Nitrate -> Water Change


As fish eat, digest, and metabolize protein, they produce waste as ammonia (NH3), which is then excreted into the water. Ammonia is also produced when excess food or other organic matter (such as a dead fish) rots in the tank. Ammonia is a small, soluble, and very active molecule. This means that it can be quite toxic to fish, even in small amounts.

Build-up of toxic ammonia within the tank is prevented in two ways. Prior to establishing a full community in an aquarium, a tank must be “cycled” with just a few fish. This allows time for ammonia-clearing (nitrifying) bacteria to establish a colony and combat the rising ammonia levels. Once a stable aquarium community is established, waste levels should be kept to a minimum. If at any time the bacterial colony becomes overwhelmed with waste, as with overfeeding, or when dead fish are left in the tank, ammonia levels might skyrocket and kill the fish.

Various commercial products are available to lower ammonia levels in an aquarium, from liquid drops to pellets that can be added to a filtration system. It is important to consider, however, that a healthy aquarium needs a good colony of nitrifying bacteria, and nitrifying bacteria need ammonia to feed on. Ammonia-removing products should only be used in emergency situations, and never relied on over the long term.


Ammonia (NH3) is continuously changed back and forth to ammonium (NH4+) in the water. The equilibrium between these two chemicals is such that nitrogen is present mainly in the ammonia form at higher temperatures and pH. Test kits are available to measure the level of total ammonia in the water, but temperature and pH are needed in order to determine how much of it is present as ammonia, and how much as ammonium. Ammonium is less toxic than ammonia, but an appropriately filtered and stocked tank with a normal amount of waste should never have an appreciable level of ammonia if a healthy colony of nitrifying bacteria has been established.


As a colony of nitrifying bacteria is established (specifically, Nitrosomnus bacteria), ammonia becomes converted into nitrite (NO2-), which is less toxic to fish than ammonia, but still lethal if levels become too high. As with ammonia, test kits are available to determine the level of nitrite in aquarium water. Testing is most useful during the initial cycling process, to help determine the extent of nitrifying bacterial colonization. Nitrite levels usually begin to rise about a week after cycling begins, depending on the size and temperature of the tank, as well as the number and type of fish being used to cycle. Testing nitrite levels is less useful in an established tank, as nitrite is only the middle step in the nitrogen cycle.


Once nitrite-producing Nitrosomnus bacteria are established, Nitrobacter bacteria begin to proliferate and convert nitrite into nitrate (NO3-). This step in the cycling process can take one to two months to complete (depending, once again, on various tank factors). Nitrate is relatively benign compared to nitrite or ammonia, and most hardy fish species can tolerate moderate levels of this chemical in the tank. Invertebrates such as corals and sea anemones are less tolerant. Nitrate is removed from the aquarium during partial water changes, the frequency of which is usually determined by a yellow discolouration of the water, a set schedule, or a nitrate test kit.

In a stable aquarium with minimal waste, ammonia and nitrite are rapidly converted into nitrate, and the danger of nitrite or ammonia toxicity is low. Regular testing of nitrate levels is the most useful way to monitor nitrogen waste levels in an established tank. If a sudden spike in ammonia levels is suspected, such as with sudden fish deaths or accidental overfeeding, emergency water changes and/or commercial ammonia-neutralizing additives can be used to lessen the impact.

To prevent unnecessary fish stress and deaths, be sure to cycle every new aquarium with one or two fish for at least a month before adding more individuals. Time should be allowed between new additions to give the bacterial population a chance to compensate for the increase in waste. Finally, keep a regular schedule of partial water changes and water quality testing, and always track down the source of an unexpected increase in nitrogen levels.

By Jen Perret – writer

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