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A high-rate nitrogen removal process is required to maintain the water quality in aquaculture tanks used to produce high-density fish populations in recirculating aquaculture systems. In this study, a combined pilot-scale system of down-flow hanging sponge (DHS) reactors and upflow sludge blanket (USB) reactors was applied as a nitrogen removal system for a longtooth grouper Epinephelus bruneus recirculating aquaculture system. The DHS reactors demonstrated high total ammonium nitrogen (TAN) removal efficiencies and the TAN concentration in the aquaculture tank was maintained at 0.32 ± 0.12 mg-N·L−1. The USB reactor fed with sodium acetate acted as a denitrification unit and adjusted the pH through denitrification reaction. All E. bruneus survived the entire experimental period and the daily weight gain rate of 0.6%·day−1 was comparable to that in marine aquaculture. This result shows that the DHS-USB system to be a novel applicable system for nitrogen removal processes in recirculating aquaculture systems and further study at a large scale should be recommended.