Ammonia and nitrite toxicity are two leading causes of fish death, especially in new aquariums. Ammonia is a byproduct of protein digestion and is excreted from the gills of fish. Fecal matter, uneaten food and decaying organisms also contribute to the ammonia load. Ammonia causes gill damage by impairing oxygen uptake and salt balance in the fish's body. It increases the potential for secondary infections by bacteria and parasites.
For more information, please read Ammonia and Water Quality.