Flooding is a serious issue in cities experiencing rapid urban growth. However, flood damage can be reduced by taking an account of flood risk assessment. The purpose of this paper is to simulate urban flooding and to evaluate the flood risk by coupling hydrologic-hydraulic modeling in the Marikina-Pasig River Basin and Metro-Manila city, the National Capital Region (NCR), in particular. We used a FLO-2D model and simulated the flood inundation of Typhoon Ondoy in August 2009. The results show that population density is highest in the west of NCR, which leads to an increased vulnerability of flooding in that area. However, more than 75 percent of the NCR boundary is classified in the moderate vulnerability level. The maximum flood depth in the city was simulated up to 10 meters, mostly in the moderate vulnerability area, whereas in the upstream of the basin the maximum flood was estimated at more than 15 meters. The results also show that areas of severe vulnerability in NCR could be submerged up to three meters. We can conclude that improvement of the river systems, controlling of the floods in the upstream of the Marikina river and diversion of excess waters from the Marikina and San Juan Rivers before they enter into the Pasig River could protect the vulnerable area of Metro Manila city.