What is aquarium filtration?

Filtration in your aquarium is essential. An aquarium filter must always be running in the aquarium.

A filter provides the following 3 functions:

  1. Mechanical filtration (mandatory): the filter media (sponge, ceramic rings) sucks up the larger particles and retains them;
  2. Chemical filtration (optional and temporary): for example, activated carbon (fish tank charcoal) is placed in a bag or in a special compartment of the aquarium filter to eliminate odor, treatment residues, heavy metals and chlorine. It is not normally used permanently.
  3. Biological filtration (mandatory): this process, invisible to the naked eye, is essential to keep aquarium fish healthy. Please read the info below: why is filtration essential for a healthy aquarium?
Lareg external filter
Small power filter
Filter media (sponges of different density)
Ceramic filer media (ceramic rings)
External canister filter (1) and internal power filter (2). The biological efficiency is best when the volume of filter media is large. Very small filters should be avoided for a goldfish tank as goldfish produce lots of waste and need a good biological filtration. Examples of filter medium: sponge (3), ceramic rings (4), filter cartridges, poly pad, etc

Why is filtration essential for a healthy aquarium?

The nitrogen cycle

As soon as they are introduced into the aquarium, fish will start to produce a significant quantity of organic waste, in particular toxic ammonia, through excreta, urine and respiration.

Fortunately, the filter’s highly porous medium (filter sponge for example) is capable of harboring billions of useful ‘cleaning bacteria‘, which are also present in the gravel and decoration. These useful bacteria will transform the highly toxic ammonia into another slightly less toxic substance, nitrite, and finally transform nitrite into nitrate, which is not very toxic except in high doses (to keep it at a reasonably low level, simply change part of the water weekly). This series of transformations is carried out in a continuous “loop” in the aquarium: this is called the nitrogen cycle.

The problem is that when a new aquarium starts, it is almost sterile: the bacteria cannot do their “cleaning” function properly because they are still too few in number… As a result, ammonia and  nitrites that are very toxic to fish build up. This is sometimes referred to as the new tank syndrome.

In case of new tank syndrome, it is essential for the health and survival of fish:

  • to make frequent partial water changes to dilute the ammonia and nitrite concentration in the aquarium. Inexpensive ammonia and nitrite tests are available in any good pet store. Easy to use, these water tests will let you know if your tank has a high level of ammonia or nitrite and to decide when a water change is necessary. Use a water conditioner (dechlorinator) when making water changes.
  • to feed the fish as reasonably as possible in order to limit the amount of waste produced in the aquarium (if the ammonia or nitrite levels are very high, stop feeding the fish for a few days).
  • to start with a limited fish number so that your filter can gradually adapt to waste production.
  • to properly oxygenate the tank (with an air filter if necessary) because beneficial Nitrosomonas bacteria are aerobic, which means they need oxygen to live and multiply.
  • you may also add commercial bacterial activators, such as Prodibio Biodigest, Tetra Bactozym or Denitrol.
Ammonia water test

Testing the ammonia level is easy and quick thanks to commercial tests (here from Sera)


  • Avoid cleaning the filter media (sponge, etc) with tap water. The chlorine contained in tap water is a powerful bactericide. In order to preserve the filter bacteria, always wash the filter sponge with water from the aquarium.
  • Avoid adding new fish until the nitrogen cycle is fully established, be patient.
  • Avoid putting too many fish at once in the aquarium

After a few weeks (4 weeks on average), bacteria are established in sufficient numbers to effectively treat the fish waste: the nitrogen cycle is then established (0 ammonia and 0 nitrite).

Aquarium Nitrogen Cycle (aquarium filtration basics)

The nitrogen cycle (summary): transformation of ammonia into nitrite by the Nitrosomonas bacteria and then into nitrate by the Nitrospira bacteria. Nitrates, which are much less toxic, are the final product of the cycle. To keep nitrates at a reasonably low level in the aquarium, a weekly partial water change is carried out. In addition, plants can use some of the nitrates as fertilizer. Illustration: Eliashc and Ilmari Karonen (public domain).

Montée des toxines dans un nouvel aquarium

Rise of toxins in a new aquarium (new tank syndrome)

The graph above illustrates the rapid rise in ammonia concentration followed by a sharp drop that shows that Nitrosomonas bacteria have multiplied and reduced ammonia to nitrite. Nitrites increase thereafter very quickly: the Nitrospira bacteria then take over by finally transforming the nitrite into nitrate. It is impossible to give a precise rate or time scale because these values vary greatly from one aquarium to another.

Warning signPossible symptoms of ammonia and nitrite poisoning in a new tank are:
(Caution: fish do not necessarily show all the symptoms at once!)

  • Fish gasping
  • Fearful behavior, clamped fins
  • Darting and scratching: the fish rubs against the decoration or stones, looks nervous, tries to jump out of the water or escape an invisible predator
  • Veined or red spots on tail or fins
  • Black smudges on fish skin
  • Respiratory problems for nitrites (nitrites limit oxygen uptake by fish and irritate their gills). Labored breathing. Sometimes, bright red gills with possible bleeding and rapid breathing.
  • Feed little or not at all
  • Simultaneous and unexplained death of several fish or unusual behavior of several fish at once.

New tank syndrome? Click here for help and solutions »

Question marksWhat is fish-less cycling?
Fish-less cycling is a method of maturing (or cycling) a new biological filter before fish are introduced. This alternative method of setting up the nitrogen cycle is a popular option because it does not involve any potential risk to the first fish.

More information about the fish-less cycling method (external link).