An integrated management system was developed for the efficient operation of a storm water treatment unit to assist in the management of urban river water quality and flow. The SWMM hydrological model was calibrated and then used to predict the hydrograph and concentration graphs of surface runoff from a storm events based on weather forecasts. These results are used to decide how to operate the first flush treatment unit in the field by comparing water quality in the unit with that in runoff. This water quality monitoring system will also be used to reflect real-time field conditions, which will be used to improve the efficiency of the treatment system. The first flush treatment unit can be installed underground to use for storage of storm water. The system was tested against field data collected in a sub-basin of the Gwanpyung-cheon stream in Daejeon, Republic of Korea. Continuous monitoring results indicated that the first 4 hours of surface runoff exhibit higher concentrations than normal levels in the study site, and these levels can be used to determine the necessary volume for efficient treatment. When settling in the treatment system over 24 hours, the average removal efficiencies for TSS, TP and TN were 87.4%, 57.3%, and 43.6%, respectively.