Ammonia is a substance toxic to all vertebrates and is found in the aquatic environment. While ammonia may be present in tap water, most of the ammonia found in an aquarium is produced by the fish. Ammonia is the primary waste metabolite produced by fish from the catabolism of protein contained within the feed. A second source of ammonia in the aquarium is decomposition of uneaten food, although this should be considered a relatively minor source. In the aquatic environment, ammonia exists in two forms in equilibrium: as unionised ammonia, NH₃, and as ionised ammonium, NH₄⁺. Thus, total ammonia concentration is the sum of the concentrations of un-ionised ammonia and ionised ammonium. The percentage distribution of each form is highly dependent upon the pH. Increasing pH results in an increase in the fraction of unionized ammonia (see graph).

Nitrate (NO₃) is produced from the oxidation of nitrite by the bacteria Nitrobacter spp. (Lewis & Morris 1986). Nitrate within aquaria is generally dismissed as not being a threat to the health of fish, although many aquatic species are sensitive to high nitrate concentrations. There are indications that toxicity of nitrate is related to its effect on osmoregulation at high ion concentrations.