Groundwater is the most important resource for local society and the ecosystem in the semi-arid Hailiutu River catchment. The catchment water balance was analyzed by considering vegetation types with the Normalized Difference Vegetation Index (NDVI), determining evapotranspiration rates by combining sap flow measurements and NDVI values, recorded precipitation, measured river discharge and groundwater levels from November 2010 to October 2011. A simple water balance computation, a steady state groundwater flow model, and a transient groundwater flow model were used to assess water balance changes under different land use scenarios. It was shown that 91% of the precipitation is consumed by the crops, bushes and trees; only 9% of the annual precipitation becomes net groundwater recharge which maintains a stable stream discharge in observed year. Four land use scenarios were formulated for assessing the impacts of land use changes on the catchment water balance, the river discharge, and groundwater storage in the Bulang catchment. The scenarios are: (1) the quasi natural state of the vegetation covered by desert grasses; (2) the current land use/vegetation types; (3) the change of crop types to dry resistant crops; and (4) the ideal land use covered by dry resistant crops and desert grasses, These four scenarios were simulated and compared with measured data from 2011, which was a dry year. Furthermore, the scenarios (2) and (4) were evaluated under normal and wet conditions for years in 2009 and 2014, respectively. The simulation results show that replacing current vegetation and crop types with dry resistant types can significantly increase net groundwater recharge which leads to the increase of groundwater storage and river discharges. The depleted groundwater storage during the dry year could be restored during the normal and wet years so that groundwater provides a reliable resource to sustain river discharge and the dependent vegetations in the area.