Flash flood hazard assessments, mitigation measures, and water harvesting efforts in desert environments are often challenged by data scarcity on the basin scale. The present study, using the Wadi Atfeh catchment as a test site, integrates remote sensing datasets with field and geoelectrical measurements to assess flash flood hazards, suggest mitigation measures, and to examine the recharge to the alluvium aquifer. The estimated peak discharge of the 13 March 2020 flood event was 97 m³/h, which exceeded the capacity of the culverts beneath the Eastern Military Highway (64 m³/h), and a new dam was suggested, where 75% of the catchment could be controlled. The monitoring of water infiltration into the alluvium aquifer using time-lapse electrical resistivity measurements along a fixed profile showed a limited connection between the wetted surficial sediments and the water table. Throughflow is probably the main source of recharge to the aquifer rather than vertical infiltration at the basin outlet. The findings suggest further measures to avoid the negative impacts of flash floods at the Wadi Atfeh catchment and similar basins in the Eastern Desert of Egypt. Furthermore, future hydrological studies in desert environments should take into consideration the major role of the throughflow in alluvium aquifer recharge.