Ammonia is the principal nitrogenous waste released by fish and is mainly excreted across the gills as ammonia gas. Ammonia is a byproduct of the digestion of protein. Bacteria in the biofilter convert ammonia to nitrite and nitrite to nitrate, a process called nitrification. Both ammonia and nitrite are toxic to fish and are therefore major management problems in recirculating systems. Ammonia in water exists as two compounds: ionized (NH4+) and un-ionized (NH3) ammonia. Un-ionized ammonia is extremely toxic to fish. The amount of un-ionized ammonia present depends on pH and temperature of the water.

In many recirculating systems, some de-nitrification seem to occur within the system that keeps nitrate concentrations below toxic levels. De-nitrification is the bacteria-mediated transformation of nitrate to nitrogen gas, which escapes into the atmosphere.