The Aquarium Nitrogen Cycle aka Biological Filtration

The aquarium nitrogen cycle

Topic Overview

The biological process, known as the nitrogen cycle, breaks down organic waste, which accumulates inside the aquarium.

Understanding the nitrogen cycle leads to greater success in caring for aquarium fish. Therefore, we highly recommend familiarizing yourself with this basic, yet important biological process.

What is the Nitrogen Cycle?

The nitrogen cycle is the natural biological process responsible for breaking down waste in the aquarium, making the water safe for the fish.

Waste dissolves in the aquarium and kickstarts a biological process, which utilizes naturally occurring bacteria. During this multi-step process, nitrifying bacteria ultimately convert organic waste into nitrate.

Three Stages Complete the Nitrogen Cycle Process

Stage 1

Adding fish to a new aquarium kick starts the nitrogen cycle. During this initial stage, waste quickly breaks down into ammonia. This waste primarily consists of fish excrement and uneaten fish food.

Stage 2

Now that ammonia is present, nitrosomonas bacteria multiply and colonize in the aquarium. Nitrosomonas bacteria oxidize the available ammonia and produce nitrite as a by-product.

Stage 3

During the third and final stage of the nitrogen cycle, nitrobacter bacteria convert the newly formed nitrite into lesser toxic nitrate.

It is important to understand that the nitrogen cycle is an ongoing process, which is essential for healthy fish life. Once ammonia and nitrite are no longer detectable, the “cycling” of the aquarium is complete, however the process does not stop.


A biologically healthy aquarium should never have detectable ammonia or nitrite. If either is present, it is because of a bacterial imbalance.

A balanced aquarium continues to efficiently break down dissolved waste, without raising ammonia or nitrite to detectable levels.

Why is the Nitrogen Cycle Important?

Without a functioning nitrogen cycle, the aquarium would turn into a toxic stew unable to support fish life.

Because an aquarium is a closed-loop eco-system, waste will accumulate.

Introducing fish, plants, and food to your aquarium begins the nitrogen cycle. Food consumed by fish provides them with energy, which they burn with the help of the oxygen they breathe from the water. As a result of this energy burning process, fish return carbon dioxide and nitrogenous compounds back to the water.

Maintaining healthy aquarium conditions, requires removal of these substances.

Carbon dioxide mainly dissipates through aeration at the surface of the tank, or through photosynthesis by aquarium plants.


Ammonia and nitrite are highly toxic for fish, therefore it is imperative that the nitrogen cycle is stable and balanced.

The nitrogen cycle eliminates toxic nitrogenous compounds as described above. Highly toxic ammonia is converted to nitrite, while toxic nitrite is converted into lesser harmful nitrate. 

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.

What are the Ideal Aquarium Conditions for the Nitrogen Cycle?

The efficiency of the nitrifying bacteria involved in the nitrogen cycle, depend on the aquarium’s water conditions.

  • 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).
  • Major changes in the aquarium’s bio-load will effect the bacteria population. For example, adding several new fish at once, may require an increase in nitrifying bacteria to deal with the increased pollution caused by these fish. This may trigger a renewed cycling process, during which ammonia and nitrite can temporarily spike, while bacteria colonies grow to meet the new waste conversion needs.

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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 »

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