AbstractAquaculture is an economic activity that faces the unavoidable problem of water quality detriment, which is mainly generated by the improper management of production ponds, including inadequate water circulation and aeration, accumulation of undigested food residues, excretion of metabolic by‐products by the cultivated organisms and other. In addition, the increase in suspended organic matter together with the presence and generation of nitrogen compounds can severely affect the physiology of the animal, leading to significant losses in production. Ammonia (NH3), nitrite (NO2) and nitrate (NO3) are toxic in different scales and environmental conditions; therefore, reducing their concentrations in the culture units has paramount relevance. In this regard, bioflocs are an efficient alternative to transform nitrogen compounds into a non‐toxic form, taking advantage of the capabilities of the microbial communities conforming them. Also, nitrogen can be harnessed and incorporated as organic nitrogen, making the biofloc a source of useful natural food for the cultivated organism. The substantial reduction in the rate of water exchange favoured by the biofloc technology (BFT) is a beneficial advantage for both the production systems and the environment, diminishing the risk of introducing pathogens into the pond in parallel with the improvement in the water quality of effluents. Ammonia oxidation is an advantage adding value to the BFT systems and is discussed in this review.