Nitrogen cycle

Aquarium filtration: the Nitrogen cycle

It is very important to understand the Nitrogen Cycle in order to set up and maintain a healthy and safe environment for your fish. To understand the nitrogen cycle, it is also important to first have a good understanding of how your filter works.

Filters work in three main ways – MECHANICAL, CHEMICAL AND BIOLOGICAL.


Mechanical filtration is the perhaps easiest to understand; it simply means that solids are filtered out of the water by straining through the filter medium – sponge, filter wool, etc. In doing this, however, the filter becomes clogged up with the solids it is straining out of the water and will require cleaning at regular intervals to remain effective.


Chemical filtration generally means any type of filtration which will alter the chemical composition of the water and remove harmful chemicals within the water. Within the aquarium this usually refers to activated carbon or, less commonly, some resins. Activated carbon removes harmful chemicals from the water by chemically absorbing them. The carbon will eventually become saturated and will need replacing or re-charging.


Biological filtration is, arguably, the most important of the three main types. Harmful chemicals deposited in the water by the livestock in the aquarium are converted biologically into less harmful chemicals by ‘friendly’ bacteria. This action is what is known as the ‘Nitrogen Cycle’.

The Nitrogen Cycle

Nitrogen cycle
Nitrogen cycle

When you first introduce fish to a new aquarium, the main problem is not the solid waste produced by the fish, it is the ammonia(NH3) released into the water. This is very toxic to the fish. The first of our friendly bacteria to spring into action are the Nitrosomonas bacteria. These bacteria derive all the energy they need for growth and reproduction from converting ammonia into nitrites. They live in several places such as soil, sewage, fresh water, etc. and they thrive in places where there are high levels of nitrogen compounds. These bacteria need large amounts of energy to divide and multiply and, because of this, it takes a while for them to develop in the aquarium in such numbers as to be of use. It is, therefore, very important that you do not stock a new tank to capacity immediately when it is set up. Patience is a virtue and a minimal stocking level is needed to begin with (one fish or maximum two or three fish depending on the size of the aquarium and the size of the fish).


Once your first fish are installed and begin to feed, they will produce toxic ammonia and carbon dioxide (CO2) from their gills and solid waste matter. Ammonia is also introduced into the aquarium by decaying matter such as solid fish waste, uneaten food and dead plant matter. Nitrosomonas bacteria present in the water will begin to convert the ammonia into nitrites (NO2) and, in doing this, will begin to multiply. As the numbers of Nitrosomonas increase and the ammonia levels correspondingly decrease, nitrite levels in the water will rapidly start to increase.

Nitrite is almost as dangerous to fish as ammonia and this is where the second batch of ‘friendly’ bacteria come into action – the Nitrobacter. These microscopic rod-shaped bacteria begin to colonise the filter and feed on the nitrites (NO2) produced by the Nitrosomonas bacteria. They convert them to nitrates (NO3) which are far less harmful to fish and other animals. In doing this they, too, begin to multiply their numbers until a balance is achieved.

The byproducts, then, of this cycle are the carbon dioxide exhaled by the fish and the nitrates produced by the bacteria. Both of these are used up to some degree by any aquatic plants present. The carbon dioxide is used up by the plants in the action of photosynthesis which produces oxygen back into the water and the nitrates are consumed by the plants as fertiliser to aid their growth.

In an ideal world, there would be nothing further to say but, because we have aquariums primarily to keep our fish, the stocking level of fish in relation to plants is almost always too high on the side of the fish – there is nothing wrong with this but it does mean that there will be more nitrates produced than the plants will need. Also, in some cases, people set up aquariums without plants or with plastic plants as decoration. This means that gradually, over a period of time, nitrates will build up in the aquarium to unacceptable levels. It is for this reason that we perform partial water changes on our aquariums at regular intervals.

As a final thought, when you clean out the filter in your tank to remove the solid wastes that build up and clog it, it is vital that you use water taken directly from the tank to do so. This is obviously best achieved at the same time as you do your partial water change, thus utilising the old water taken from the tank to clean your filters out with. The reason for this is that if you use tap water to clean out your filter, the chlorine and chloramines added to the water by the water board are deadly to the colonies of bacteria in the filter media. The obvious conclusion to this is that when you replace the filter media, not only have you killed all the bacteria in it and disrupted the all-important nitrogen cycle, you have also introduced a large quantity of dead bacteria into your aquarium which will decay and add to the chemical imbalance caused by the disruption.

For the same reasons, it is most important when performing a partial water change to ensure that you never use new untreated tap water. Always de-chlorinate the water you use, either by letting it stand for 24 – 48 hours with aeration or by using a proprietary tap water conditioner / de-chlorinator available at all good aquatic shops. It is worth noting that leaving the water to stand will remove chlorine but not chloramines and in this instance, a tap water conditioner is advised.

Source: (no longer available)

Last Updated on 29 May 2020 by John

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