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Why is an understanding of the nitrogen cycle important when setting up a fish aquarium?

Article ID: 454
Last updated: 19 Sep, 2016
Revision: 5
Views: 28590

Filtration in aquariums can be mechanical (using sponges to collect debris), chemical (to absorb specific toxins) or biological (to break down fish waste). Effective biological filtration and healthy plant growth is critical for a healthy and sustainable aquarium.

Biological filtration

To keep fish healthy and happy, a good quality biological filter is required to breakdown toxic aquarium waste products such as fish waste, food waste and decaying plants. This process is commonly referred to as the ‘nitrogen cycle’ or ‘nitrification cycle’ and refers to the establishment of beneficial bacterial colonies which break down waste products into less harmful compounds. There are three stages of the nitrogen cycle and every new aquarium must go through these three stages before biological filtration is fully functioning.

The largest contributing factor to fish loss/death in aquariums is a failure to understand this process and provide the right conditions for it to occur. In a new aquarium (or new filter) there are not enough beneficial bacteria to eliminate all toxins immediately, so for a period of two to six weeks, steps need to be taken to reduce risks to fish health and welfare and  to prevent fish deaths.

The three stages of the nitrogen cycle

First stage - ammonia

  • Fish waste forms ammonia, which is highly toxic to most fish. In a new aquarium ammonia levels usually begin rising by the third day after introducing fish.

Second stage - nitrite

  • As nitrite-forming bacteria (nitrosomas) develop, ammonia is converted to nitrite and while the ammonia levels decrease, nitrite levels increase. Nitrite levels usually begin rising by the end of the first week after introducing fish.

Third stage – nitrate

  • As nitrate-forming bacteria develop (nitrobacters), nitrite levels decrease and nitrate levels increase. When nitrates are being produced and ammonia and nitrite levels are zero, your tank is fully cycled and your biological filter is fully functioning (from 2-6 weeks). In low levels, nitrates are not highly toxic to fish. Routine partial water changes of about 10% should keep nitrate levels within a safe range.

Tips for a healthy aquarium

Beneficial bacteria grow on any surface in the aquarium and they are concentrated in the filter sponge/media which has a high surface area. By constantly flowing water through the filter, ammonia and nitrite are rapidly converted to nitrates, assisting in keeping tank water free of toxic levels of these compounds. You should avoid completely cleaning a tank as this will remove the beneficial bacteria. Instead, partial water changes of approximately 10% should be performed once per week, using a gravel vacuum to remove waste and uneaten food from the substrate. At this time the sides of the tank can be wiped with an aquarium safe sponge and filter media and/or decorations can be cleaned in old tank water.

Regularly test your water for ammonia, nitrite & nitrate levels to ensure your biological filtration is sufficient, you are maintaining it appropriately and your aquarium is not overstocked or overfed.

Your filter is ultimately only as effective as the media it contains. There are many types of biological media available on the market and it is important to select a media which has a high biological capacity.

Do not add large numbers of fish to your aquarium at any one time - gradual introduction will enable the filtration bacteria to slowly adapt.

Please note that in marine/saltwater aquariums fishless cycling and using live rock to cycle the aquarium is often recommended.

Further information is available from the following website:

Marine Aquarium Societies of Australia

If you need specific advice on how to safely cycle a tank, please consult an experienced aquarist or fish veterinarian for further advice about how to safely cycle a tank. 


This website provides general information which must not be relied upon or regarded as a substitute for specific professional advice, including veterinary advice. We make no warranties that the website is accurate or suitable for a person's unique circumstances and provide the website on the basis that all persons accessing the website responsibly assess the relevance and accuracy of its content.
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