This paper investigates the issues and challenges in using a 3D city model for monitoring flash flood risks in Salalah (Oman) designed using the City Geography Markup Language (CityGML) standards version 2.0. The investigation was made based on the fact that 2D and 2.5D GIS solutions cannot analyse flood complex problems inside the urban area. Hence, the study sought to reduce time and effort for the decision-makers by proposing a 3D city model for flood risk management. The study used geospatial tools and databases such as ArcGIS, Watershed Modelling System (WMS), FME, PostgreSQL-PostGIS, and 3D City Database (3DCityDB) to generate the 3D model and to test the capability of establishing a unified geospatial data structure including the 3D city objects, hydrological data, and geological data. The findings showed the importance of addressing flood risks data and arranging it in the 3D geodatabase. It was also revealed that establishing a 3D city model based on the CityGML standard requires homogenised definitions and standards for city objects (surface and subsurface) as well as hydrological data.