The sustainability and efficiency of flood risk management depends on the assessment of flood hazards and on the quantification of flood damage. Under the conditions of climate change and rapid urbanization, the evaluation of flood risk can lead to the success of adaptation strategies. The main objectives of this study are the estimation of future direct flood damage in two urban watersheds: The Pasig-Marikina-San Juan River in Metro Manila, Philippines, and the Ciliwung River in Jakarta, Indonesia, as well as the determination of the relation between factors that drive floods and flood damage. A spatial analysis approach based on the integration of several parameters, such as flood hazard, climate, and property value, was applied using a Geographic Information System (GIS). The flood depth-damage function generated from the field surveys was employed for the analysis to identify the spatial distribution of flood loss. The findings showed that, under future scenarios (target year: 2030), the total flood damage will increase by 212% and 80% in the target areas of Manila and Jakarta, respectively, compared to the current scenarios. This growth is due to the higher level of extreme rainfall events and to the degree of urbanization in the future. A comparative analysis of the two study areas highlighted the significant effects of the level of water depth and the inundated areas on flood damage, depending on the sites. This study is useful for local decision makers to implement suitable strategies for urban planning and flood control.