For the effective operation of irrigation reservoirs, a general and systematic policy is suggested to make balance of the conflicting purposes between water conservation and flood control. In this study, the flood effective analysis system was developed through the integration of long-term water budget analysis model, GIS-based HEC-HMS model and HEC-RAS model. The system structure consists of long-term water budget model using modified TANK theory, flood runoff and flood effects analysis model using HEC-GeoHMS, HEC-HMS and HEC-RAS models. The flood effects analysis system simulated the flood runoff from the upstream, downstream flood and long-term runoff of the watershed using the observed data collected from 1998 to 2002 of Seongju dam. The simulated results were reasonably good compared with the observed data. The optimal management method of the reservoir during the whole season is suggested in this study, and the flood analysis system can be a useful tool to evaluate a reservoir operation quantitatively for the mitigation of flood damages of reservoir basin.