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It determines the quality of ammonia produced in aquacultural systems by direct excretion from the fish and by breakdown of organic compounds by hetrotrophic bacteria as the first inorganic compound produced through nitrogen cycle, ammonia is then oxidized to nitrate (NO2) by several bacterial species, the mostly commonly known genus of which is Nitrosomonas. Nitrate is then further oxidized by several group of bacteria, mostly widely known of which in Nitrobacter, nitrate (NO¬3). The rate at which the conversion of ammonia to nitrate takes place depends on nitrogen concentration in water, oxygen concentration, organic concentration in water in filter, temperature, and other variables.

Ammonia is the major end product of protein breakdown in fish. Fish digest the protein in their feed and excrete ammonia through their gills and in their feces. The amount of ammonia excreted by fish varies with the amount of feed put into the pond or culture system, increasing as feeding rates increase. Ammonia also enters the pond from bacterial decomposition of organic matter such as uneaten feed or dead algae and aquatic plants.