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Karst aquifers in semi-arid regions are particularly threatened by surface contamination, especially during winter seasons when extremely variable rainfall of high intensities prevails. An additional challenge is posed when managed recharge of storm water is applied, since karst aquifers display a high spatial variability of hydraulic properties. In these cases, adapted protection concepts are required to address the interaction of surface water and groundwater. In this study a combined protection approach for the surface catchment of the managed aquifer recharge site at the Wala reservoir in Jordan and the downstream Hidan wellfield, which are both subject to frequent bacteriological contamination, is developed. The variability of groundwater quality was evaluated by correlating contamination events to rainfall, and to recharge from the reservoir. Both trigger increased wadi flow downstream of the reservoir by surface runoff generation and groundwater seepage, respectively. A tracer test verified the major pathway of the surface flow into the underground by infiltrating from pools along Wadi Wala. An intrinsic karst vulnerability and risk map was adapted to the regional characteristics and developed to account for the catchment separation by the Wala Dam and the interaction of surface water and groundwater. Implementation of the proposed protection zones for the wellfield and the reservoir is highly recommended, since the results suggest an extreme contamination risk resulting from livestock farming, arable agriculture and human occupation along the wadi. The applied methods can be transferred to other managed aquifer recharge sites in similar karstic environments of semi-arid regions.