World Heritage sites in general are exposed to the impacts of natural hazards, which threaten their integrity and may compromise their value. Floods are a severe threat to the Angkor World Heritage site. Studies of regional floods and flood hazard zoning have played an increasingly important role in ensuring sustainability of the Angkor site. This study developed a flood hazard index (FHI) model based on a geographic information system (GIS) and used synthetic aperture radar (SAR) data to extract historical floods at Angkor from 2007 to 2013. Four indices (flood affected frequency, absolute elevation, elevation standard deviation, drainage density) were used to identify flood-prone areas. The Analytic Hierarchy Process (AHP) and the Delphi method were employed to determine the weight of each index. The weighted indices were then used to develop a distribution map of flood hazards at Angkor. The results show that 9 monuments are at risk by potential floods among the 52 components of the Angkor monuments. The high hazard and moderate-to-high hazard areas in the core zone are mainly located surrounding the West Baray but will not bring direct risk impact on the monuments located in the core archaeological zone. The moderate hazard areas are located on both sides of the Siem Reap and Roluos rivers and in the flooded area of the Tonle Sap Lake in the core archaeological zone. These areas cover 19.4 km2, accounting for 9.13% of the total area of the core zone. This moderate hazard zone poses a greater flood threat to the core zone and must be given higher attention. The buffer zone is a small area with fewer sites. As such, flooding has a low impact on the buffer zone. The methods used in this study can be applied to flood hazard assessments of other heritage sites in Southeast Asia.