The Aquarium Nitrogen Cycle Explained: Ammonia to Nitrate

The aquarium nitrogen cycle is the chain of microbial reactions that turns toxic ammonia from fish waste into nitrite, and then into much less toxic nitrate. The microbes that do this grow slowly, live mainly on filter media and other surfaces, and need oxygen and alkalinity to work. Nitrate is the end product in most tanks, so it builds up until you remove it with water changes or plant growth.

The three compounds at a glance

Compound	Formula	Where it comes from	Why it matters
Total ammonia	NH3 + NH4+	Fish excretion through the gills, decaying food and waste	Un-ionized NH3 damages gills; any reading in a cycled tank signals a problem
Nitrite	NO2−	First oxidation step	UF/IFAS lists toxicity in fish at levels as low as 0.10 mg/L
Nitrate	NO3−	Second oxidation step	Far less toxic, but accumulates in closed systems

According to the UF/IFAS fact sheet Ammonia in Aquatic Systems, ammonia is the most important water quality factor for fish after oxygen. Most of it leaves the fish by diffusion across the gills, and even a fish that is not eating produces some. That same publication notes that nitrate was long considered harmless even at 200 mg/L, but more recent research suggests it may be more harmful than previously thought. In closed systems it can exceed 250 mg/L without water exchange.

Step one: ammonia to nitrite

Textbooks usually credit this step to ammonia-oxidizing bacteria (AOB) such as Nitrosomonas and Nitrosospira. Those organisms are real and important in many systems, but studies of actual home aquarium filters complicate the picture.

A 2011 survey by Sauder and colleagues used gene-based methods on 27 freshwater aquarium biofilters and found that ammonia-oxidizing archaea (AOA, members of the Thaumarchaeota) outnumbered AOB in 23 of them. In 12 filters, archaea accounted for all detectable ammonia-oxidizer genes. The share of archaea was higher in tanks with lower ammonium concentrations. A follow-up study tracking six freshwater tanks over four months (Bagchi et al., 2014) again found archaea dominant in every freshwater filter and noted they grew preferentially on fine sponge. In the one marine tank studied, bacteria outnumbered archaea by orders of magnitude.

The practical takeaway is modest: a mature, lightly loaded freshwater filter may rely on a different community than a freshly started, ammonia-rich one. It does not change how you cycle or maintain a tank.

Step two: nitrite to nitrate

For decades the nitrite oxidizer in aquarium literature was Nitrobacter. Work led by Timothy Hovanec and published in 1998 (Hovanec et al.) examined freshwater aquarium biofilms and found Nitrospira-like bacteria were the organisms associated with nitrite oxidation; Nitrobacter was not detected in the established filters they studied. The appearance of Nitrospira DNA lined up with the point at which nitrite began to drop.

This helps explain a familiar pattern during cycling: ammonia starts falling within a week or two, but nitrite can stay high for another week or more while the nitrite oxidizers catch up.

Comammox: one organism doing both steps

Since the 1890s nitrification had been treated as a two-organism job. In 2015 two independent teams reported in Nature that some Nitrospira can carry out complete ammonia oxidation to nitrate on their own, a process now called comammox. Daims et al. cultivated such a bacterium, Candidatus Nitrospira inopinata, and van Kessel et al. enriched two comammox Nitrospira species from a recirculating aquaculture system.

Comammox organisms have since been found in aquaculture filters. A study of a commercial freshwater recirculating aquaculture system in operation for more than 15 years (Bartelme et al., 2017) found a stable nitrifying community built around ammonia-oxidizing archaea and comammox Nitrospira, with Nitrobacter not detected. How much comammox contributes in a typical home aquarium has not been well quantified, so treat it as an interesting finding rather than something to manage.

Why it is not really a cycle

In nature, nitrate is taken up by plants and algae or converted to nitrogen gas by denitrifying bacteria in low-oxygen sediments. A typical aquarium has only a little of either. That is why the “cycle” in most tanks is a one-way conveyor ending at nitrate, and why regular water changes remain necessary. Fast-growing plants can take up a meaningful share, though rarely all of it in a well-stocked tank. To size your changes, see water change math.

Ammonia versus ammonium: the pH and temperature effect

Ammonia test kits measure total ammonia, which is a mix of toxic un-ionized ammonia (NH3) and much less toxic ammonium (NH4+). UF/IFAS states NH3 is roughly 100 times more toxic than NH4+, and its share rises with both pH and temperature. The factors below come from the UF/IFAS table (based on Emerson et al., 1975); multiply total ammonia by the factor to estimate un-ionized ammonia.

pH	68°F (20°C)	78.8°F (26°C)	82.4°F (28°C)
7.0	0.0039	0.0060	0.0069
7.4	0.0098	0.0150	0.0173
7.8	0.0244	0.0370	0.0423
8.2	0.0590	0.0880	0.0998

Worked example: a total ammonia reading of 1.0 ppm at pH 7.0 and 78.8°F gives 1.0 × 0.0060 = 0.006 mg/L NH3. The same reading at pH 8.2 gives 1.0 × 0.0880 = 0.088 mg/L, about 15 times more. UF/IFAS advises that tissue damage can begin above 0.05 mg/L un-ionized ammonia. This is why a small ammonia reading is more urgent in hard, alkaline water than in soft, acidic water.

What speeds up or slows down the bacteria

Temperature

Nitrifiers grow faster in warm water and slow down markedly as water cools. Tropical tanks usually cycle faster than unheated ones, and a coldwater tank or pond filter can lose capacity in winter. A sudden large temperature drop can temporarily reduce how much ammonia a filter processes.

pH and alkalinity

Nitrification releases acid, which consumes carbonate alkalinity (KH). Standard wastewater-engineering stoichiometry puts this at about 7.1 mg of alkalinity (as CaCO3) per mg of ammonia-nitrogen oxidized. UF/IFAS notes that common nitrifiers do not function effectively below a total alkalinity of about 20 mg/L, and that once alkalinity is gone pH can fall quickly, the pattern called “old tank syndrome.” Low pH also shifts ammonia toward ammonium, which protects fish but slows the classic ammonia oxidizers. Our GH, KH, and pH explainer covers how to keep buffering stable.

Oxygen

Both steps are aerobic. UF/IFAS recommends acting if dissolved oxygen drops below 5 mg/L. A clogged filter, a power cut, or a filter left switched off for hours can starve the colony of oxygen.

Chemicals

UF/IFAS warns that some disease treatments, especially antibiotics, can harm biofilter bacteria, and recommends testing ammonia and nitrite more often after treatment. Always follow the medication label and consult an aquatic veterinarian where possible.

Reading units correctly

Scientific papers and some kits report nitrogen compounds “as N.” Most hobby kits report the whole ion. Mixing them up causes large errors, especially with nitrate.

To convert from	To	Multiply by
Ammonia-N (NH3-N)	NH3	1.22
Ammonia-N	NH4+	1.29
Nitrite-N (NO2-N)	NO2−	3.28
Nitrate-N (NO3-N)	NO3−	4.43

For example, 10 mg/L nitrate-N equals about 44 mg/L as nitrate ion.

Putting it to use

• A new tank needs a steady ammonia source to grow this community. The fishless cycling guide walks through the 2 ppm method, and the dosing calculator works out how much to add.
• Most of the colony lives on surfaces, especially filter media. Rinse media in removed tank water rather than chlorinated tap water, and avoid replacing all of it at once.
• Keep KH above roughly 3 to 4 dKH (about 54 to 71 mg/L as CaCO3) if your fish tolerate it, well clear of the 20 mg/L floor.
• If fish are already in an uncycled tank, see cycling with fish safely.