The Nitrogen Cycle

Nitrogen is the most abundant element in the atmosphere where it is harmless. Through a series of chemical processes, nitrogen from the atmosphere is incorporated into animals and plants through the food chain. In the marine aquarium, nitrogen comes from waste products of fish and other animals. Three forms of nitrogen are important for the marine tank:

  • Ammonia – a very toxic form of nitrogen in the waste products of fish; if not removed quickly, ammonia will kill fish.
  • Nitrite – a by-product of the breakdown of ammonia; at high levels is toxic to fish.
  • Nitrate – a safer form of nitrogen that results from the conversion of nitrite; however, nitrate can build up to toxic levels and must be removed through regular water changes

Although we often think of bacteria as harmful, certain types of beneficial bacteria in the marine aquarium convert very toxic ammonia into nitrite and then to nitrate. Nitrate is safe for fish at low levels, which are maintained by regular water changes and the breakdown of nitrate to nitrogen gas which re-enters the atmosphere.


Even in a new tank, there will be small colonies of the different types of bacteria that “engineer” the nitrogen cycle. Before your tank is ready for a full collection of fish, you need to feed these bacteria. It may seem odd, but the process starts by adding ammonia, the form of nitrogen we are trying to avoid.


There are a few ways to jump start the nitrogen cycle. Perhaps the best method is to add pure ammonia from a bottle, though you should be careful to ensure there are no additional chemicals added to the bottled ammonia. Another method is to “feed” the empty tank by adding food or a piece of dead fish or shrimp to the tank that will decay and naturally release ammonia. Finally, if you absolutely cannot wait to put fish into your tank, you can add a one or two hardy fish (such as a tank-raised clownfish) that will add ammonia to the tank through their waste products. Take care if choosing this method, though, as it is easy to overload the tank, resulting in dangerous ammonia levels. Feed these starter fish lightly so bacteria will build up gradually.


While cycling your aquarium, you should be regularly monitoring its progress by performing water tests to track the ammonia, nitrite, and nitrate levels. Most likely, the ammonia level will probably increase for the first week or so. You may start to see the water cloud up slightly, which is a sign that the bacteria are increasing. Over the next few weeks, ammonia in the water will decline and nitrite will increase. At that time, different bacteria that feed on nitrite will start to grow and begin to convert the nitrite into nitrate. Once the ammonia and nitrite levels have dropped back down to zero, the tank will be ready to add some fish from the Buyer’s Guide list. You should change out 10-25% of your tank’s water every few weeks to keep the nitrate at a safe level.

Thanks to Michael Griffith of Segrest Farms for his contribution to this article.