Controlling toxic nitrogenous substances in biofloc technology (BFT) systems is critical for the success of this novel technology. To effectively control nitrogen accumulation in BFT systems, it is important to first understand the dynamics and the removal pathways of this element and its related compounds from aquaculture water. This review focuses on synthesizing the information of nitrogen dynamics in BFT systems to provide researchers and practitioners with a guide to the fate of nitrogen and its control methods. This paper discusses the different types of nitrogenous compounds in BFT water, the transformation processes of ammonia to nitrites and nitrates, the relationship between the two forms of ammonia (NH3 and NH4+) in water and the equilibrium between them. This paper also discusses nitrification as a major nitrogen removal pathway and the factors that influence the nitrification process. Notably, the control of nitrogen in BFT systems by manipulating the carbon to nitrogen ratio (C/N) using external carbohydrates is described in this paper. This paper suggests that further studies should focus on investigating the various factors that influence nitrogen dynamics in BFT systems and the means of controlling contaminants other than nitrogen.