Guide to nitrogen cycle in aquarium

The nitrogen cycle is an integral part of the existence of any aquarium. The nitrogen cycle refers to the cycle of ammonia, nitrites, and nitrates. Plants, aquarium inhabitants, and bacteria, i.e. all components of an aquarium biosystem. If you want to know why your aquarium gets cloudy, keep reading.

All you need to know about nitrogen cycle NH3 / NH4 +, NO2- and NO3-


What is nitrogen and where does it come from in an aquarium?

Nitrogen is found in protein molecules, peptides, amino acids, chlorophyll, ribonucleic acids, vitamins, etc. The main supplier of nitrogen in the aquarium is fish food, as protein in the composition of the feed is usually 40 – 50%. Fish after eating, excrete urea, and excrement. Other organic waste, such as dead plant leaves, can also be a source of nitrogen. All โ€œorganicsโ€ are processed by heterotrophic bacteria, fungi, protozoa, and nitrogen from proteins that are converted to amino acids and other components, including ammonium [NH4 +]. Some of the ammonium can be absorbed by plants, the remaining amount undergoes further transformations.

Watch this video to understand how an aquarium with extremely high amount of nitrogen looks:


Differences between ammonia [NH3] and ammonium [NH4 +]

Ammonia in water can be present in two forms – as ammonia itself [NH3] and as an ammonium ion [NH4 +]. Ammonia [NH3] is extremely toxic to fish; even when it is contained in the water at about 0.05%, chronic gill damage occurs in fish. The toxicity of ammonium [NH4 +] is significantly lower. That is, if there is mainly ammonium in the water, then the fish will not be poisoned, but if there is the same amount of ammonia, then the outcome is likely to be sad.

The percentage of ammonia and ammonium in the water directly depends on the acidity level (pH) of the water. At pH = 6.5, the ammonia content is approximately 0.1%. At pH = 7 – 0.5%. Far with increasing pH, the value of ammonia begins to grow in catastrophic sizes. At pH = 8, it is already 5%, and at pH = 8.4 it is already 10%. At pH = 9, ammonia may already be all 40 – 50%.


Ammonia oxidizes to ammonium at pH <7

The activity of nitrifying bacteria that oxidize ammonia is also affected by water temperature. The higher the temperature, the greater the proportion of toxic ammonia. At 28 ยฐ C, twice as much toxic ammonia than at 20 ยฐ C (at equal pH).

If you still have problems understanding the nitrogen cycle I can recommend you to watch the first 2 minutes of this fantastic short video explaining it: Be careful this video has SOUND!

HOW TO: Cycle an Aquarium (Nitrogen Cycle)


The process of converting ammonia [NH3] โ†’ to nitrite [NO2โ€”] โ†’ and then to nitrate [NO3โ€”] is called the nitrification process.

Bacteria involved in the nitrification process can be located anywhere in the reservoir, but in the aquarium, they are concentrated mainly in the external filter, in the upper soil layer and other places with a good flow: here aerobic bacteria find an influx of nutrients and a sufficient concentration of oxygen.

Ammonia conversion occurs with the help of bacteria of the genus Nitrosomonas and Nitrosococcus, which, with sufficient oxygen in the water, oxidize ammonia to nitrites. Nitrifying bacteria require a large amount of oxygen, so they are also called aerobic. To oxidize one milligram of ammonium [NH4 +] to nitrite, 1.5 mg of oxygen is needed. In this case, a molecule [NO2โ€”] (nitrite) + two hydrogen ions [2H +] + water molecule [H2O] + energy, which was actually needed by the bacteria, is formed. This unique oxidation is possible only by bacteria. Nitrite is slightly better than ammonia, but also very toxic. The permissible concentration is 0.1 mg / l, but not more than 0.2 mg / l; the readings above are life-threatening to fish.

Further, aerobic bacteria of the genus Nitrospira and Nitrobacter also oxidize nitrites [NO2โ€”] to nitrates [NO3โ€”] with the participation of oxygen. Here oxygen is already required much less – about 0.5 mg. Nitrates are significantly less toxic (dangerous, as a rule, at a concentration of 50 mg / l), although in large quantities they lead to a decrease in immunity, a deterioration in color, and further to fish death. Excess nitrates are removed from the aquarium with a simple change of water. Do not forget to regularly change the water in the aquarium!


The conversion of nitrate [NO3โ€”] back โ†’ to nitrite [NO2โ€”] and then โ†’ to gaseous nitrogen [N2] is called the denitrification process.

Denitrification occurs only in anaerobic, oxygen-deficient areas of the soil, which are usually located at a depth of more than 1 cm. Denitrification is a microbial transformation by bacteria of the genus Pseudomonas, Paracoccus, or Bacillus. [NO3โ€”] nitrates are not at all the final decomposition product of ammonia [NH3]. They are used by anaerobic, denitrifying bacteria to extract oxygen. Some nitrates are converted by anaerobic bacteria back to nitrites, which are oxidized to nitrogen during processing [N2]. If nitrogen, in this case, is not consumed by the roots of the plants, then it will dissolve in the water and disappear into the atmosphere.

Plant roots can deliver oxygen to the soil, preventing it from complete anaerobicity. In a substrate of coarse gravel, there will be no anaerobic conditions at all. In a substrate mixed from the gravel of various sizes, local oxygen-free (anaerobic) denitrification zones are most likely to form.

Nitrification cycle

Aquarium fish poisoning with ammonia, nitrites, and nitrates

Symptoms of ammonia poisoning:

  • Lack of oxygen and difficulty breathing
  • Lack of coordination of movements and attempts to jump out of the water
  • Darkening body-color
  • Damage to gills

Symptoms of nitrite poisoning:

  • Rapid breathing – fish stay on the surface of the water and breathe with difficulty
  • Cramps, especially in small fish
  • The tissues of the gills instead of the normal healthy bright red color may acquire a completely different color – from purple to brown
  • In a few hours or days – depending on the endurance of this species – death may occur

Symptoms of nitrate poisoning:

  • Fish become lethargic
  • Gills turn pale, suffocation occurs, which leads to the death of the fish


If there was a sharp jump in ammonia or nitrite, then the fish immediately need to be transplanted into fresh water. In the case of nitrate poisoning, the substitution of aquarium water, with the use of aquarium chemistry (conditioners), can help. Be sure to check the concentration of all three parameters in the aquarium into which you intend to launch new fish, using testing and, if necessary, immediately take corrective measures.


To prevent poisoning, you need to think about the filter performance + aquarium capacity + the number of fish + amount of feed given to fish. Leftover food, dead fish, and other organic waste should be removed immediately from the aquarium. The reduction in the content of all three parameters in aquarium water is ensured by high-quality filtration and suitable filtering material (fillers of external filters to remove NH3, NO2โ€”, NO3โ€”).

Watch this on-point shortย video about fish ammonia poisoning treatment: Be careful this video has SOUND!

How To Get Rid of Ammonia In Your Aquarium