A flash flood is one of the hazardous phenomena, especially in dry regions. In Saudi Arabia, Jazan Province experiences data scarcity especially historical hydrological data and a lack of studies related to flash flood analysis and the rainfall and runoff interrelationship. Thus, this research aims to study the rainfall-runoff inter-relation, predict flash floods, and to map the risk areas in Jazan Province by the geological, geomorphological, and hydrogeological characteristics along with digital elevation model (DEM), watershed modeling system (WMS) and HEC-HMS models. Jazan Province encompasses 25 drainage basins, receiving a considerable amount of rainfall (ranging from 100 to 500 mm) (August, October-November, March) which intermittently cause strong and destructive flash floods. The DEM was used for delineating the catchment (drainage basins) parameters. Physiographic parameters of the catchments have been analyzed for mapping the hazard degree of the flash flood strength. Further, basins with high hazard degrees of flash floods were selected to assess rainfall-runoff inter-relation using the HEC-HMS models, GIS, and morphometric parameters. Forty %, 8%, 52% of the study area are high, medium, and low hazard degrees of flash floods, respectively. The groundwater recharge in the study area was calculated through the integration of satellite image analysis, SWAT and GIS techniques and it ranges from 0.002 mm/km2/year to 8 mm/km2/year with an average of 2.5 mm/km2/year. Rainfall-runoff inter-relation of study basins, assessed based on the integration of WMS and HEC-HMS models, indicates that the resulting runoff volume ranges from 18.5 × 106 m3 to 473.1 × 106 m3 at a recurrence period of 5 and 100 years at rainfall events of 65 mm and 116.8 mm, respectively.