Ammonia is the primary nitrogenous (protein breakdown) waste product excreted by fish and is also produced when organic matter, including uneaten food, decomposes in water. Ammonia is generally either in the toxic unionized form or the non-toxic ionized form. The ratio between the two compounds depends on temperature, pressure, salinity, and most importantly, pH (number of hydrogen ions dissolved in the water). Generally, the higher the pH, the more unionized (harmful) ammonia is present. The total ammonia nitrogen (TAN) reading represents both forms. A TAN measurement of 3.0 parts per million (ppm) would be deadly at a pH of 8.5 but relatively harmless at a pH of 6.0. Hobbyists and professionals alike commonly ask at what point should ammonia levels be considered dangerous? The best answer is that any detectable ammonia in an established aquarium indicates a filtering deficiency. Either the filter is inadequate for the system or the biological load is too great for the filter.

Affected aquarium or pond fish will frequently be anorexic (not eating), lethargic (slow or depressed), and may have "clamped fins." They may also swim erratically, and can be found "piping" at the surface for air or bolting from one side of the aquarium to the other. Some fish produce excessive mucus in response to the elevated ammonia and may appear cloudy or pale. The eyes may be opaque and the gills pale or swollen. The aquarium or pond water is frequently cloudy and in some cases dead fish and uneaten food may be present (contributing to the problem). Morbidity (illness) and mortality (death) can be quite high. Frequently, the aquarium or pond may have been recently established. This situation is commonly referred to as "New Tank Syndrome." If ammonia toxicity occurs in a mature system, new fishes may have been added without increasing filtration. Another common finding in the medical history is a change in the management of the system (a new person is feeding the fish, the type and amount of food has changed, the frequency of water changes has decreased, dead plants and fish are not removed immediately).

The exact physiological mechanism of ammonia toxicity in fishes is unknown. We do know that when aqueous ammonia levels are elevated, blood and tissue levels of ammonia rise. This situation may lead to decreased oxygen transport by the blood, an increase in blood pH, and an osmoregulatory disturbance for the fish.