Ammonia is the first by-product generated during the Nitrogen Cycle and the most toxic. It is produced from the breakdown of solid wastes such as faeces, food remains, decaying plant leaves and the metabolic process of the fish themselves, excreted as pure ammonia across the gills. Ammonia causes osmoregulatory damage (see osmosis for a full explanation) and is an irritant to delicate tissues such as the internal organs. As a cellular toxin, ammonia is very effective and can perform fatal damage within days.

Ammonia exists in two forms, the toxic ammonia molecule (NH3) and the non-toxic ammonium ion (NH4+). When pure ammonia (NH3) dissolves in water, it forms both ammonia (NH3) and ammonium (NH4+) via a process known as dissociation i.e. some of the ammonia has been neutralised. The extent of dissociation depends on the pH and temperature of the water.

Look at this example:

If water is pH 7.0 at a temperature of 25°C, 0.55% of the ammonia in solution is in its toxic pure form. However, raise the pH to 8.0, at the same temperature, 5.28% is toxic. An increase of one on the pH scale increases the toxicity of ammonia by ten times!

Keeping the pH constant this time at say pH 7.5, and varying the temperature from 15°C to 20°C increases the toxicity from 0.85% to 1.25% an increase of 68%.

You may be thinking that because your aquarium has a low pH your fish are safe. Think again. A fish's blood is around pH 7.2-7.5. Thus if ammonia is present within the tissues of a fish it will become more toxic due to the increased pH of the blood. Fish do have some buffering capacity to protect against the effects of the ammonia produced through its own metabolism but "high" levels are still dangerous.

The ideal total ammonia level (NH3 plus NH4+) is 0 mg/l or parts per million (ppm). At a level of 0.25 mg/l most fish will not survive more than 3 days. If ammonia is present at 1.5 mg/l it is unlikely that the fish will see the next day and levels of 5mg/l are almost certainly fatal within 24 hours.

An indication of the effects of ammonia poisoning is when fish gulp air from the surface. Be aware that some fish such as labyrinth fish and some Corydoras sp. will do this naturally. If in doubt test for ammonia using a test kit.