The nitrogen cycle
The single most important process in a freshwater aquarium. Everything a fish excretes, and everything that decays in the tank, enters the water as ammonia. A mature aquarium hosts microbial populations that oxidise it in two steps, keeping ammonia and nitrite near zero. Establishing those populations is 'cycling', and adding fish before it is done is the commonest cause of early losses.
In one sentence
Bacteria and archaea in the filter and on every surface convert ammonia from fish waste into nitrite, and nitrite into far less toxic nitrate, which is removed by water changes and plants.
The two oxidation steps
Ammonia-oxidising microorganisms convert ammonia (NH₃) and ammonium (NH₄⁺) to nitrite (NO₂⁻). A second group converts nitrite to nitrate (NO₃⁻). Both steps consume oxygen and both release hydrogen ions, which slowly consumes carbonate hardness and pushes pH down over time.
The organisms involved are not the ones named in older aquarium literature. Nitrosomonas and Nitrobacter dominate wastewater textbooks, but studies of freshwater aquarium filters have generally found Nitrospira to be the principal nitrite oxidiser, and ammonia-oxidising archaea are also present. The practical advice is unchanged; the names in older sources are not reliable.
| Stage | Compound | Toxicity | Target in a stocked tank |
|---|---|---|---|
| Input | Ammonia / ammonium | High — depends strongly on pH and temperature | 0 mg/L |
| First oxidation | Nitrite | High — interferes with oxygen transport | 0 mg/L |
| Second oxidation | Nitrate | Low at aquarium concentrations | Kept low by water changes |
Where the bacteria actually live
Very little of the population is free in the water. The great majority lives as biofilm on surfaces, with the filter media providing most of the available surface area. This is why replacing all the filter media at once removes most of the biological capacity, and why a filter left switched off for a few hours begins to lose it as the oxygen runs out.
- Rinse filter media in tank water, not under the tap — chlorinated water kills the biofilm.
- Replace media in stages, never all at once.
- A filter switched off for more than about an hour should be rinsed before restarting, because the material inside it goes anaerobic.
Where the nitrogen goes next
Nitrate accumulates unless it is removed. In most aquariums water changes do the removing. Fast-growing plants take up meaningful quantities of nitrogen, and in a heavily planted tank they can hold nitrate down without much intervention. Denitrification to nitrogen gas happens only in anoxic zones, which are present in deep substrates and inside some filter media but are not something a typical tank can rely on.
Common misconceptions
| Often said | What is actually the case |
|---|---|
| Cycling means running the filter with no fish for a few weeks. | Bacteria need an ammonia source. A filter running in an empty tank with nothing to process develops almost no population. Cycling requires ammonia to be added, whether from a bottle or from a fishless source. |
| A cycled filter stays cycled if the tank is empty. | The population is sized to the ammonia supply. Remove the fish for two weeks and the capacity falls to match. Restock gradually afterwards. |