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In (semi-)arid regions, available water resources are scarce and groundwater resources are often overused. Therefore, the option to increase available water resources by managed aquifer recharge (MAR) via infiltration of captured surface runoff was investigated for two basins in northern Jordan. This study evaluated the general suitability of catchments to generate sufficient runoff and tried to identify promising sites to harvest and infiltrate the runoff into the aquifer for later recovery. Large sets of available data were used to create regional thematic maps, which were then combined to constraint maps using Boolean logic and to create suitability maps using weighted linear combination. This approach might serve as a blueprint which could be adapted and applied to similar regions. The evaluation showed that non-committed source water availability is the most restricting factor for successful water harvesting in regions with <200 mm/a rainfall. Experiences with existing structures showed that sediment loads of runoff are high. Therefore, the effectiveness of any existing MAR scheme will decrease rapidly to the point where it results in an overall negative impact due to increased evaporation if maintenance is not undertaken. It is recommended to improve system operation and maintenance, as well as monitoring, in order to achieve a better and constant effectiveness of the infiltration activities.