Ammonia accumulation is a critical issue in aquaculture systems due to its toxic effects on aquatic organisms, including reduced growth, increased oxygen demand, and elevated mortality. Approximately 78% of nitrogen in aquaculture systems originates from protein-rich feed, with only 25% contributing to animal growth and the remainder excreted as waste, ultimately forming inorganic ammonia. This article explores three primary ammonia transformation pathways: assimilation by photoautotrophic algae, oxidation by autotrophic nitrobacteria, and assimilation by heterotrophic bacteria. Among these, heterotrophic assimilation forms the basis of Biofloc Technology (BFT), an innovative approach that uses added carbon sources to stimulate microbial biomass growth, which efficiently uptakes ammonia while improving water quality. In contrast, Recirculating Aquaculture Systems (RAS) primarily rely on autotrophic nitrification for ammonia control, requiring precise management of oxygen, pH, and alkalinity. While RAS offers enhanced biosecurity and reduced water use, challenges remain in nitrate accumulation and system complexity. This review highlights the advantages and limitations of BFT and RAS, offering insight into sustainable ammonia management strategies for high-density aquaculture operations.