This study aims to investigate the flow conditions in the proposed canal system to be located in Songdo District, Incheon. Incheon Free Economic Zone (IFEZ) is concerned about the potential issues like water quality and algal problems, which will greatly affect the success of the Songdo waterfront development.Thus there is a need to ensure that natural stream flow and good water quality will maintain. In order to do this, a 3D numerical model, MIKE 3 FM was setup and used to investigate the water circulation system with respect to the operation of the four water gates present at the ends of the canal system, where ideal configurations of the gate operations were determined. The model was computed water quality change under various tidal conditions. The results given by the numerical model will be used as indications for a preconstruction plan of the Songdo canal system.By annual period simulation using real measured data from Incheon coast, analyse the polluted water from songdo city’s land inflow which is large influence to canal water quality. BOD, Nitrogen and phosphorous parameter from land are increased and influence to WQI(Water Quality Index). In canal WQI is 3~4 points that is higher than costal WQI which is increased by polluted water from land inflow. So we analyse the water quality change impacted by polluted land inflow and suggest a method to alleviate polluted water in Songdo waterfront’s canal system. Acknowledgments This research was supported by a grant (12-TI-C01) from Advanced Water Management Research Program funded by Ministry of Land, Infrastructure and Transport of Korean government.