Historical records show that Baubau City experienced 20 floods between 2009 and 2018, inundating approximately 1,206 community buildings. To minimize similar impacts in the future, this study aimed to identify areas prone to flooding in the Baubau Watershed for return periods of 5 to 100 years. The initial phase of the study involved determining the design flood discharge based on analysis of 10 years of rainfall data using the Nakayasu Synthetic Unit Hydrograph method. Through field surveys, data on river hydrological conditions and watershed morphometric parameters were obtained. These data were then analyzed using a hydraulic model using HEC-RAS 5.0.7 software and subsequently exported to HEC-GeoRAS as part of the spatial processing in ArcGIS 10.5. The integration of hydrological and hydraulic models in this study resulted in estimates of physical, social, and economic losses, as well as spatial maps of flood-prone areas in three sub-districts: Murhum, Batupoaro, and Wolio. These three areas are spread across seven urban villages along the Baubau River and have a high risk of flooding.