Ammonia is the primary waste product of fish, excreted primarily through the gill tissue, but to a lesser extent via the kidney. Ammonia can also accumulate from the decay of fish tissues, food and other organic debris derived from protein. Ammonia accumulations cause reddening of the skin and disability of the gills by its direct caustic effect on these surfaces. Fish suffering in water with high ammonia accumulations will isolate themselves, lie on the bottom, clamp their fins, secrete excess slime, and are much more susceptible to parasitic and bacterial infection.
Ammonia is a big problem in new systems because the bacteria that would naturally dissolve ammonia are not established, see discussion of cycle. As well, even in established systems, ammonia may accumulate in springtime when the water is cold but fish are eating, because filter bacteria have not emerged usefully from hibernation.
Ammonia is capable of ionization below pH 7.4 and so in its ionized state is less toxic to fish.
Above pH 8.0 most ammonia is ionized, and so becomes more toxic. Care should be taken not to increase the pH of a system if ammonia is present but the need to drop the pH or restrict oxygenation to tanks of fish to keep pH down is an overrated aberration in the literature.
Treatment: Water changes (with Dechlor) and management of the pH near neutral will go a long way to cutting losses from Ammonias, ancillary, less useful modes of Ammonia management include the use of the various water conditioners that bind ammonia, and the application of rechargeable Zeolites to the system filter. I am still going to tell you that time and water changes are the two mainstays, however.
Water that is warm, high in pH (There’s a test) or deprived of oxygen will have an enhanced toxicity when ammonias are accumulating. These are all important considerations as we try to interpret the varying symptomatology of fish at the same ammonia level, for example, but are affected very differently.