The purpose of this study is to ensure optimal operating conditions for improving the removal efficiency of phosphorus (P) and nitrogen (N) that are the causative agents of eutrophication by utilizing functional media. The main ingredients of the functional media used in this study are Si, Al, and Fe, SiO2, KAlSiO3O8, Al2O2·2SiO2O, H3Al2Si2O9, Fe3O4O), and berylite. To identify the maximum efficiency of the filtration process, the processing efficiency experiment was carried out according to flow method, velocity, and thickness of residual media. The flow method carried out two experiments, 50 m/day, 100 m/day, 150 m/day, 200 m/day, 250 m/day, and 20 cm, 40 cm, 50 cm, 60 cm, 80 cm of lead depth. Experiments have shown that SS, T-N, and T-P all showed higher elimination efficiency of the upflow current conditions than the downflow current conditions, and that the processing efficiency of the linearity is the highest at SS 50 m/day, T-N 150 m/day and T-P 100 m/day. In addition, the analysis of the removal efficiency according to the residual thickness showed that SS, T-N, and T-P all showed the highest efficiency at 60 cm. In addition, the analysis of the removal efficiency according to the residual thickness showed that SS, T-N, and T-P all showed the highest efficiency at 60 cm. It is considered desirable to set the top-down flow conditions and residual thickness of 60 cm and adjust the velocity of the line according to the target media for removal.