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Many hydrological approaches have been developed for humid areas; however, we still have many challenges regarding flash floods simulation in arid regions. Thus, the main purpose of this study is to develop a physically based hydrological model for flash floods simulation, to understand the hydrological processes, and to overcome the water relating problems, as water scarcity, data deficiency. In this study, Hydrological River Basin Environmental Assessment Model incorporating wadi system (Hydro-BEAM-WaS) integrated with both Geographic Information System (GIS) and remote sensing data is proposed. To overcome the lack of observational data, Global Satellite Mapping of Precipitation (GSMaP) data has been compared with the Global Precipitation Climatology Center (GPCC) data. We found that the GSMaP has an overestimated or underestimated systematic seasonal bias. Wadi El-Khoud in Oman was chosen for model calibration, while the River Nile basin in Egypt was chosen for flash flood simulations. The simulation has been successfully carried out where it exhibits a reasonable fit between both the simulated and observed results, in spite of the deficiency of high quality observations. This approach can be used to evaluate and simulate the wadi runoff behaviors, such as discontinuous surface flow. It also can help in estimating the initial and transmission losses. Flash flood water has been assessed and evaluated as new water resources, which would be properly utilized to overcome the problem of water shortage in such regions. The proposed model has been proven to provide reliable simulations of flash floods referring to ungauged wadi systems.