Flooding is a natural disaster with extensive impacts. Desert regions face altered flooding patterns owing to climate change, water scarcity, regulations, and rising water demands. This study assessed and predicted flash flood hazards by calculating discharge volume, peak flow, flood depth, and velocity using the Hydrologic Engineering Centre-River Analysis System and Hydrologic Modelling System (HEC-HMS and HEC-RAS) software. We employed meteorological and morphological data analyses, incorporating the soil conservation service (SCS) curve number method for precipitation losses and the SCS-Hydrograph for runoff transformation. The model was applied to two drainage basins (An-Nawayah and Al-Rashrash) in southeastern Cairo, Egypt, which recently encountered several destructive floods. The applied model revealed that 25-, 50-, and 100-year storms produced runoff volumes of 2461.8 × 103, 4299.6 × 103, and 5204.5 × 103 m3 for An-Nawayah and 6212 × 103, 8129.4 × 103, and 10,330.6 × 103 m3 for Al-Rashrash, respectively. Flood risk levels, categorised as high (35.6%), extreme (21.9%), and medium (21.12%) were assessed in low- and very-low-hazard areas. The study highlighted that the areas closer to the Nile River mouth faced greater flood impacts from torrential rain. Our findings demonstrate the effectiveness of these methods in assessing and predicting flood risk. As a mitigation measure, this study recommends the construction of five 10 m high dams to create storage lakes. This integrated approach can be applied to flood risk assessment and mitigation in comparable regions.