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This paper aims to propose methods to mitigate the risks of flash flood events in arid rural communities with poor infrastructure. A flash flood management case study was conducted at Afouna Village in Egypt, which is characterized by an arid climate and faced a devasting flash flood in 2015. First, the flash flood was modelled and it was found that it corresponds to a 100 year return period flood that led to an almost 13 million m³ total runoff volume. A structural protection approach, using an artificial infiltration pond, was applied to mitigate the flooding risks through water harvesting and recharging the groundwater of the Moghra aquifer. In this study, a novel approach was proposed, which is substituting the low permeability silty sand (2.0 × 10⁻⁴ m/s) in the pond area with a high permeability one (9.6 × 10⁻³ m/s), which will enhance water harvesting and reduce direct evaporation. Modern techniques of hydrological modelling were utilized in order to achieve the optimal use, and harvesting, of flash flood water.