In the natural ecosystem habitats of most common tropical fish, the presence of toxic levels of nitrogen-containing compounds is relatively rare. In an aquarium environment, however, there is often overfeeding and overcrowding in a small, contained space. These fully closed environments are conducive to nitrogen pollution that can sicken or even kill your aquarium fish. These are the basic compounds and processes that make up the nitrogen cycle.
The natural nitrogen cycle is a full cycle where nitrogen goes from air to plant to animal to bacteria and back to air; such a system needs no human intervention. In an aquarium though, the nitrogen process is less a cycle and more a biochemical cascade that involves the continual chemical degradation of nitrogenous compounds from ammonia to nitrite to nitrate. The final nitrates are then taken up by aquarium plants or removed from the water by other means.
This cascade describes how natural wastes in the water get processed in natural ecosystems. And even in a closed aquarium, this cascade must be established and fostered by the hobbyist. Ammonia, nitrite, and nitrate are the main biological toxins that occur in an aquarium, so the nitrogen "cycle" must work effectively to convert and remove all of these waste byproducts.
In a living aquarium, this cascade is established over time. It usually takes up to three months before a new aquarium has fully converted its wastes into nitrate. The method of stocking your new aquarium slowly over time with younger, smaller fish is meant to allow the nitrogen converting bacteria time to grow, to keep pace with the gradual increase of waste matter.
Fish urea and proteins get immediately converted by bacteria (step 1) into ammonia. Under normal conditions, ammonia is a colorless, pungent gas that is highly toxic. When ammonia gets too high, it's because there are too many fish in the aquarium or the fish are being fed more than they need for healthy survival. But in an aquarium kept in balance, bacteria called "nitrogen-fixing bacteria" will then eat (oxidize) this ammonia (step 2), changing it to nitrite.
Nitrites are the most common killers of aquarium fish so they are the compounds to guard against in the nitrogen cycle. Nitrites occur in the aquarium through the partial oxidation of ammonium ions. Nitrite-loving bacteria then convert the nitrite into nitrate (step 3), thereby rendering it mostly harmless.
The simplest first step in preventing nitrite build-up is to feed sparingly, making sure there are not too many animals in the tank. Secondly, carry out a partial water change regularly (not exceeding 20% of the total volume) with well-aged water, not tap water.
Third, make sure there are not too many total living animals in the aquarium. Many who are new to the aquarium hobby forget that even though catfish, algae eaters, and snails are “cleaner fish,” each still produces waste and adds to the total nitrite.
Nitrates are the end-product of the oxidation of nitrogen compounds. In the aquarium, nitrates are produced mainly through the breakdown of animal protein and ammonium compounds. Examples include urine, excrement, foodstuffs, and the remains of dead fish, snails, and plant leaves.
Most freshwater tropical fish and other aquarium inhabitants are very tolerant of even large quantities of nitrates. However, precautionary measures to prevent too high a build-up of nitrates include feeding sparingly and maintaining a small animal population.
Because they actively use nitrogen, aquatic plants can greatly reduce the levels of nitrate in a well-adjusted aquarium as well. In a natural ecosystem, the plants remove and use nitrates. In an unplanted tank system, the tank owner must do the removal at this final stage of the cascade.