The aims of this study is to examine the effects of the changes in HRT(Hydraulic Retention Time) and media charge in a water-mill, among other operation factors, on the nitrogen and phosphorus removal in order to use up-flow anaerobic reactors, anoxic reactors and water-mill aerobic reactors for sewage treatment. The extension of HRT improved the nitrogen removal efficiency, however the removal pattern was constant regardless of HRT. The removal of phosphorus was constant (80%-90%) regardless of the change in HRT. The removal rate with change in influx load varied such that at the OLR (Organic Load Rate) of 1-3 kg/d, the T-N removal efficiency was 80.7%-88.9% and the T-P removal efficiency was 82.9%-89.3% while at the NLR (Nitrogen Loading Rate) of 0.108-0.156 kg/d the removal efficiencies were 80.7-88.9% (T-N) and 82.9-89.3% (T-P). The analyses of the nitrogen and phosphorous removal characteristics with the C/N and C/P ratio showed that the mean T-N removal rate was 88% at the C/N ratio of 1.2-2.6, and that the mean T-P removal rate was 86% at the C/P ratio of 7.2-14.1. Also, the analysis of nitrogen and phosphorous removal characteristics were analyzed in relation to media charge. The comparison between with and without media charge in the water-mill showed that while the nitrogen removal efficiencies were 86-94% and 85-89% respectively, the difference of phosphorous removal efficiencies were between the two conditions was not significant, thus it suggested that the media charge has less effect on the removal efficiency of phosphorous compared to that of nitrogen.