Jakarta has experienced many floods in the past, and those floods resulted in not only human casualties but also economic damages. In this paper a rainfall runoff and flood inundation model was applied to the 2013 flood event of the Ciliwung River basin and Jakarta by using radar rainfall information as the input. The applied model relatively well reproduced the flood inundation situation in Jakarta. As the results of analysis, we concluded that the shortage of capacity flow in the lower Ciliwung River contributed 6.7%, the shortage of capacity flow in other rivers 72.9%, and the urbanization and the land subsidence 20.4% of the total flood inundation volume in Jakarta. Furthermore, it was found that the land use change from 1983 in the target areas contributed 38% of the total flood inundation volume.