The Aquarium Nitrogen Cycle aka Biological Filtration

The aquarium nitrogen cycle

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.

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.

The entire nitrogen cycle begins with the conversion of solid wastes excreted by fish into ammonia. Bacteria known as nitrifiers include two “microbial partners” which transform toxic ammonia into nitrite and nitrate via biochemical oxidation.

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

Nitrifiers are most active at temperatures ranging from 68 – 86 degrees F. Their metabolism will decrease below 50 degrees F, while levels above 95 degrees F are potentially life threatening.

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.

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Hello, before I got fish I had my water tested and it was okay. Then I got some cichlids in my tank and algae the sequence kill my algae eater and I took it out and took it back to PetSmart now my tank is cloudy. How to use a water conditioner and a bacteria supplement but my tank is still cloudy how often should I use it it? Also took half of the water out and refilled it before I put the conditioner and bacteria supplement in. Please help!!

Please review our post about ‘New Tank Syndrome‘. Also review this additional article about ‘Aquarium Biological Filtration‘. It usually takes around 4 – 6 weeks to establish need beneficial bacteria in a new aquarium. This bacteria, called ‘Nitrifying Bacteria‘ is what helps break down organic waste in your aquarium. Unfortunately, fish death is not all that uncommon during this time, since toxic ammonia and nitrite will spike until enough bacteria have established. Doing large water changes is actually counter productive, since it can prevent or delay the balancing of your fish tank. Stick to changing no more then 15 –… Read more »

Grace rachal

Okay , I just rescued a tank from my step dads best friend and it’s been cycling for about 24 hours and the water is very cloudy . All of the levels are within safe limits accordingly to my test kits . Would it be safe to start acclimating the fish and introduce them to the tank even though the water is cloudy ?

The cycling process doesn’t really begin until fish are introduced to the aquarium. Organic waste is required for the cycling to begin. Simply put, ‘cycling’ is the process of the nitrifying bacteria breaking down dissolved organic waste (uneaten fish food, fish excrement, decaying plant mater, etc). Therefore a source of waste is needed in order to establish the required bacteria. So you should introduce fish. However, beware that the tank will go through ammonia, nitrite and nitrate spikes while the biological filter is getting established and this will likely stress the fish and may lead to fish loss. Unfortunately this… Read more »


how can i know the numbers or quantity of bacteria needed for 1 square fish tank

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.


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?

Scott @ Algone

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… Read more »

Jason M. Wester

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

Scott @ Algone

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… Read more »