Hanoi, the capital city of Vietnam, is highly vulnerable to flooding from the Red River. A flood disaster in 1971 devastated the river basin and claimed the lives of 100,000 people. The Red River dike system was built to protect Hanoi from flooding of the Red River; however, thousands of households are outside the protected area inside the dike system and are highly vulnerable to flooding. Hanoi’s flood protection measures are classified according to the water level of the Red River at Long Bien station: warning levels 1, 2, and 3 correspond to water levels of 9.5 m, 10.5 m, and 11.5 m, respectively. However, risk-reduction strategies for residential areas based on a flood hazard assessment are still inadequate. This study modeled floods and mapped them using a two-dimensional depth-averaged hydrodynamic model to show the inundation depth levels for the entire area in high resolution. Residential areas were found to be highly vulnerable to flooding at all warning levels. Outside the area protected by the dike system, 40.17% (15.94 km2), 54.08% (21.44 km2), and 79.75% (31.60 km2) of the study area were inundated at warning levels 1, 2, and 3, respectively, and these areas contain a small number of households. These results can be used to develop flood prevention and mitigation plans for Hanoi.