In closed aquaculture systems, about 10% of the fresh water enters the rearing system and the remaining 90% is supplied through water return. 10% water change is needed to compensate for the small part of water evaporation and disposal of sediments in the biological filter section. In closed systems for better management, three major tasks must be done, removal of particles and solid residues, biological filtration, aeration and disinfection of water. In fish, the most important excretory substance resulting from the metabolism of proteins is ammonium, which is found in two forms: non-toxic ammonium and toxic ammonia. There is a buffer state between these two forms, the amount of each of them depends on pH, temperature and salinity. Nitrogen compounds can be converted using the biological process of nitrification. Chemoautotrophic bacteria undergo three stages of transformation during their biological process. First, Nitrosomonas and Nitrosococcus bacteria are activated by ammonia. The waste nitrogen compounds are oxidized to nitrites. Nitrobacter and Nitrospira bacteria convert nitrite into nitrate in the second stage. In the third stage, nitrate is converted into nitrogen gas through the process of denitrification by Achromobacter and Pseudomonas bacteria, and finally leaves the system. The inoculation of these bacteria into the environment will accelerate the start of nitrification. The efficiency of biofilters in aquaculture often depends on their ability to oxidize ammonia to nitrate. The most important factors affecting the performance of bacteria and biofilters include pH, alkalinity, ammonia and nitrite, dissolved oxygen of solid materials, salinity and temperature.