Clear cloudy aquarium water, remove nitrates and simplify aquarium maintenance
Discus fish tank

The aquarium nitrogen cycle aka biological filtration

One characteristic, next to passion for the hobby, every aquarist should have or obtain, is patience.

Patience, next to understanding the basic water parameters, will be put to the test while cycling a tank. And cycling by all means, not only during the fresh set up of a new tank.

An established aquarium can cycle at any time, depending on severe changes of the bioload, filtration failure, or any loss of nitrifying bacteria.

The process of the aquarium nitrogen cycle starts the aquarium. Since an aquarium is an artificial and fragile ecosystem it requires our “interference” in order to thrive. Our interference starts with providing an “artificial” filtration system. In short, creating an environment as close to nature as possible.

The aquarium nitrogen cycle

Introducing fish, plants, and food to your aquarium begins a natural process called the nitrogen cycle. Food which is consumed by the fish provides them with energy. This energy in turn is burned with the help of oxygen which your fish breathe from the water.

During the energy burning process, waste is returned to the aquarium environment via the fish’s gills. The waste primarily consists of carbon dioxide and nitrogenous compounds such as ammonia. In order to maintain a healthy environment, these substances must be removed. The carbon dioxide is mainly eliminated through either aeration at the surface of the tank or through photosynthesis by aquarium plants. As for the toxic nitrogenous compounds, they are converted to less toxic compounds via the nitrogen cycle. Natural bacterial colonies convert ammonia into relatively harmless by-products.


Both bacteria prefer alkaline environments (pH 7.2 – 8.5). However a stable and consistent pH level is important.


Nitrifiers need oxygen to perform their task (aerobic respiration). Nitrate is the final compound after completion of the biochemical oxidation, which plants utilize as a fertilizer thus removing them from the water.

The aquarium is a well oxygenized artificial ecosystem that carries a high biomass (all living organisms) compared to nature. Often the plants are unable to utilize all the nitrates produced. In consequence nitrates accumulate, resulting in the need for regular maintenance of the aquarium in order to keep nitrate levels within acceptable parameters.

Nitrifying bacteria work either at full capacity or drift into a dormant state. Major changes in the bioload will effect the bacteria population. Additional bioload may have the effect of a new cycle (adjustment through growth). Some medications will kill bacteria, such as antibiotics, and trigger the same effect.

6 thoughts on “The aquarium nitrogen cycle aka biological filtration

    • You really can’t. You can see if you have adequate bacteria if the aquarium is healthy and balanced. Whenever the bio-load changes in the tank, the bacteria population will adjust accordingly. In other words there isn’t one specific amount of bacteria that is right for every aquarium.

  1. How can one keep track of all these elements…although it helps to observe your tank…all these things are invisible to us…I recently had a perfect tank, all levels just spot on…added 2 fish (not at same time)..and 2 new snails for a total of 5 fish…2 snails…well…I noticed some bullying going on…removed them quickly..they were nipping at the Large Fancy With long flowing tail…they did terrible damage…it seemed after that …I lost 4 of my fish…Stress killed them or the adding of more fish, more food..more decay? nitrates at level 2?..shouldn’t have killed them all?..what went wrong?

    • You can get a master test kit at any aquarium/pet store. The basic tests usually include ammonia, nitrite, nitrate, pH, and water hardness. Checking the values once a month should be adequate.

      Stress will definitely contribute to health issues and can lead to death in the aquarium. It’s impossible for us to diagnose the cause of your fish loss with the information at hand, but usually fish stress will amplify other problems in the tank. Stress will not kill but make fish more susceptible to disease. Also, nitrate isn’t usually a great concern for fish loss. Certainly you want to avoid prolonged elevated levels, however nitrate is a greater contributor to algae growth then it is to fish loss. Ammonia and nitrite on the other hand are lethal if fish are exposed for prolonged periods. Therefore they should always be undetectable. Adding too many fish at once is likely to result in a short term spike of ammonia and nitrite. But again, this shouldn’t be a problem if these spikes are brief in duration. But coupled with aggression and the resulting stress this combination could explain why your fish died.

      Be sure to speak to a knowledgeable fish store employee before buying new fish. Make sure they are compatible with what you already have. Also stock the tank slowly of time to avoid biological imbalances due to the sudden increase in bio-load.

  2. Does adding Algone to a new tank effect the cycle by removing ammonia? By removing ammonia for the BB to feed on?

    • Algone does not have a negative effect on the biological filter, the bacteria, or the cycling of the aquarium. Algone removes excessive ammonia, nitrite and nitrate. It does not stop its production, no additive is capable of doing this. Ammonia and nitrites are highly toxic for aquarium fish and therefore should always be undetectable. It should only be detectable for a brief period when breaking in a new tank. Algone will help minimize the spikes during the cycling, lessening its negative impact on fish. Sufficient bacteria will establish and break down the remaining nutrients until the tank reaches a healthy balance of beneficial bacteria and waste/nutrient production.

Leave a Reply
