This study is a geoarcheological approach to compare two ancient cities, focusing on the relation of their present water availability to their past water-storage volumes. The first is the Meroitic city of Naga in the dry savanna of Sudan, where around the turn from Before the Common Era (B.C.E.) to the Common Era (C.E.), the citizens built the “Great Hafir” with a capacity of 45 × 103 m3 to collect surface runoff. The second city is Resafa in the desert steppe of Syria, where, around 300 years C.E., the Romans built large cisterns with a total capacity of 21 × 103 m3 to store surface water. We aim to evaluate the physical catchment characters of two semi-arid watersheds and their present-day water availability by applying the rainfall-runoff model HEC HMS. The main input is contemporary rainfall data, classified through a magnitude-frequency analysis to determine rainfall intensity of one-hour events. This analysis suggests that the water reservoirs of each now long-abandoned city would be completely filled by a 35.9mm h−1 rain event in the Resafa basin and a 39.1mm h−1 rain event in the basin of the Great Hafir. Such events occur nearly annually, which in turn implies that water harvesting in the two semi-arid regions would still be feasible today.