Ammonia is produced when various organisms break down protein in order to obtain energy. Protein can come from any organic source e.g. food, fish waste or plant debris. In an aquarium, the main source of protein and thus ammonia is from fish food, whether it is eaten or not. At sufficiently high levels, ammonia is highly toxic to fishes and other aquatic life although its toxicity depends on a number of water conditions. Ammonia can be found in two forms in the aquarium; free ammonia (NH3) and ammonium ions (NH4+), of these two forms, free ammonia is by far the most toxic.
Ammonia is initially produced as highly toxic free ammonia but a large majority is converted into ammonium ions, the exact amount that remains as less toxic ammonium ions is dependant on the pH, temperature and salinity of the water. Water with a high pH level and high temperature will hold a greater ratio of more toxic free ammonia whilst water with a low pH and low temperature will have a greater ratio of less toxic ammonium ions. Water with a high salinity will hold a greater ratio of ammonium ions than free ammonia.
Under stable conditions in established aquaria with a mature filter, ammonia (both forms) will be converted by bacteria into less toxic nitrite (NO2) long before levels of ammonia become harmful. New aquariums are more prone to toxic levels of ammonia because they do not yet have a high enough population of useful bacteria to process sharp raises in ammonia production. Avoiding toxic ammonia levels in new aquaria can only be done through correct management during the maturation of the aquarium.
There are a number of situations in which ammonia levels can also quickly rise to dangerous levels in an established aquarium; some common causes are as follows:
Unnoticed deaths of sizeable fish
Power cuts causing a decrease in useful bacteria through lack of oxygen supply to filtration bacteria
Decrease in useful bacteria due to washing of biological filtration media in chlorine rich water (e.g. tapwater)
Sudden overfeeding e.g. through the use of a 'holiday' food block or drastic change in food type and frequency
Death of large numbers of snails after the use of 'snail killer' medication.
Death of useful bacteria from the use of medication

Ammonia levels
Virtually all ammonia test kits do not distinguish between free ammonia and ammonium ions and give only a reading for total ammonia. Exact levels of toxicity are therefore difficult to establish and it should also be noted that different fish have varying levels of tolerance. To ensure safe levels under all aquarium conditions and fish species, an ammonia level of zero is ideal and 0.1ppm a maximum safe level for short periods. If ammonia results show levels higher than 0.1ppm there are a number of steps that can be taken to remove or decrease ammonia back to a safe level:
Stop or significantly reduce feeding quantities for a few days
Remove organic debris from the substrate via the use of a gravel cleaner
Use a dedicated chemical filtration media designed to quickly remove ammonia e.g. zeolite or an adsorption 'pad'.
Do not replace or thoroughly clean filter media, this may remove useful bacteria
Beware of recommendations to add proprietary 'bacterial starters', which contain concentrations of 'useful' bacteria that convert ammonia. In many cases the effectiveness of these products is highly variable and although they may help to establish a filter and thus decrease ammonia in the long term, in the short term they may actually increase ammonia. This increase occurs by the overdosing of bacteria which die back and the product itself introducing ammonium compounds as a 'food source' for the bacteria.
In situations where ammonia levels have become dangerous, products are available which convert free ammonia into ammonium ions and 'lock' ammonia into the ammonium ion state. This locking process ensures that although ammonia levels will still be high, the ammonia will be far less toxic and can still be converted by bacteria in time.