The Upper Wadi Fara’ basin, located at the West Bank, Palestine, has an average annual rainfall of 500 mm, which occurs only during winter. Agriculture uses stored soil water and complimentary irrigation from groundwater. Water harvesting (WH) and managed aquifer recharge (MAR) therefore is essential for sustainable water resources management in the basin. This study focuses on the comparison between two methods to determine best practices for WH/MAR. The first method uses the change in water productivity and can be considered a one parameter cost benefit analysis (CBA). The other method concerns the multi year water allocation system (MYWAS), which uses water demand curves to evaluate economic scenarios. It is concluded that the highest cost effectiveness of WH/MAR measures in upper Wadi Fara’ basin is reached when water is stored as soil water. However, this is a politically disputed measure in the Israel – Palestine shared aquifer. Both models are useful tools in decisive stakeholder participation processes.