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Ammonia is passed from the gills of fish in their urine and rotting food or decaying plant matter are contributors of ammonia.
It exists in two forms in the aquarium and the first step is to understand the difference between ammonium NH4 and free ammonia NH3.
NH3 (ammonia) is a gas and sometimes called toxic or free ammonia. This is the type of ammonia is the dangerous part.
NH4 (ammonium) is a nontoxic salt it is the ionised form of ammonia.
NH3 and NH4 together are often refered to as total ammonia nitrogen (TAN).
Under normal conditions NH3 (ammonia) and NH4 (ammonium) will both be present in aquarium water. The two exist at an equilibrium point that is governed largely by pH and temperature. However; salinity and ionic strength of the water also have influence on this equilibrium point.
The chart below shows how the ratio between NH3 and NH4 is affected by pH in a controlled sample. As the pH increases, the ionised NH4 is liberated into gaseous NH3. As the pH increases there reaches a point where NH4 cannot exist and all ammonium is presented as NH3 ammonia; this is beyond the pH of normal aquarium life.
The blue line on the chart below indicates the pH where a marine aquarium normally fall and shows that roughly 10% to 15% of the TAN is NH3 and the rest (85% to 90%) will be NH4. Therefore, when any ammonia (TAN) is present in a normal aquarium, the majority of it will be NH4.
Tradition test kits and photometers measure TAN and as such misiterpretation what is being measured can occour. For more information please chick here.