The urban drainage model requires spatial data and catchment discretization because of the complexity of system. Using integration of Geometric Information System (GIS) technology and urban storm water models, the performance of urban drainage system can be analysed.[1] Especially in coastal area, the main problem of urban drainage is overloaded capacity because of rapid urbanization and coastal floods caused by storm surges and wave action superimposed on high water levels generated during the cycle of tides. Land use change, watershed area as settlements area, clogged drainage pipe/channel, the changing of imperviousness of land cover also contributes to large volume of surface runoff. Moreover, the developments can change land cover in urban area and increasing rainfall runoff. One of the solutions for coastal urban drainage is by using polder system for flood control. The purpose of this paper is to illustrated how GIS can model the catchment discretization and MIKE URBANSWMM (Storm Water Management Model) can analyse water balance based on the rainfall return period of 25, 50 and 100 years. The research shows evaluation result of the polder performance including inundation depth and pump performance by linking GIS between storm water models. The case study is analysing the Pluit polder in Jakarta-Indonesia, which is connected to the Indonesia Central Bank compartment. Based on the model, this polder system can reduce flooding i