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The Wadi Natuf catchment is situated to the west of the Palestinian capital city of Ramallah which is in the West Bank. The catchment has been instrumented since 2003 to identify and examine recharge processes in semi-arid upland karst terrain, in which both direct and indirect recharge are important. The key recharge processes are direct rainfall recharge, and indirect recharge via wadis including the lateral routing of potential recharge in the unsaturated zone to springs which supply the wadis. A conceptual model describing these processes was developed. A distributed recharge model was then employed to test this conceptual model and to calculate recharge. A semi-arid wetting threshold method, based on local field experiments was used for recharge estimation. The model was calibrated by comparing simulated wadi flows to those recorded during a relatively short historical event. The study demonstrates that short-term monitoring can enable a sensible validation of a conceptual model leading to the estimation of recharge. Confidence in the model simulation requires further field work to strengthen the understanding of processes taking place in semi-arid climates and karstic flow environments.