The phased isolation intra-clarifier ditch system used in this study is a simplified novel process enhancing simultaneous removal of biological nitrogen and phosphorus in municipal wastewater in terms of elimination of additional pre-anaerobic reactor, external clarifier, recycle of sludge, and nitrified effluent recirculation by employing intrachannel clarifier. Laboratory-scale phased isolation ditch system was used to assess the treatability on municipal wastewater. When the system was operated at the HRTs of 6~12hours, SRTs of 9~31days, and cycle times of 2~8hours, the system showed removals of BOD, TN, and TP as high as 88~97%, 70~84%, and 65~90%, respectively. The rainfall in Korea is generally concentrated in summer because of site-specific characteristics. Especially, the wet season has set in on June to August. In combined sewers, seasonal variations are primarily a function of the amount of stormwater that enters the system. In order to investigate the effect of hydraulic shock loading on system performance, the laboratory-scale system was operated at an HRT of 6hours (two times of influent flowrate) during two cycles (8hours). The system performance slightly decreased by increasing of influent flowrate and decreasing of system HRT. Nitrification efficiency and TN removal were slightly decreased by increasing of influent flowrate (decreasing of system HRT), whereas, the denitrification was not affected by hydraulic shock loading. However, the higher system performance could be achieved again after four cycles. Thus, the phased isolation technology for enhanced biological nutrient removal in medium- and small-scale wastewater treatment plants suffering fluctuation of influent quality and flowrate.