Aquaculture has experienced significant global expansion and is considered one of the fastest-growing sectors in food production. However, there exist additional challenges that restrict the capacity to achieve maximum efficiency in aquaculture systems, such as issues over water quality and shortages of appropriate live feeds. Intensive aquaculture systems involve the use of protein-rich prepared feed for feeding the cultured animals. This may give rise to the discharge of nitrogenous compounds into the water, which can pose a risk to the environment when present in excessive quantities beyond the acceptable levels. In recent years, an innovative method called biofloc technology (BFT) has become a practical solution to this issue. Undoubtedly, BFT offers a groundbreaking method for nutrient disposal that eradicates the requirement for excessive water use or equipment maintenance. Three primary types of microorganisms are crucial in alleviating the adverse impacts of nitrogen compounds in this technique. Photoautotrophs participate in the processes of removal and absorption, whereas chemoautotrophs promote nitrification and conversion. Heterotrophs contribute to the absorption process. Biofloc predominantly consists of heterotrophic bacteria, alongside algae, protozoa, rotifers, and nematodes. While there have been reviews carried out on multiple aspects of biofloc technology, there exists a lack of literature that tackles this particular field of research progress. This article discusses every aspect and techniques of biological management used for removing nitrogenous waste compounds in biofloc aquaculture systems.