Since groundwater is an integral component of natural hydrologic systems, an estimation of groundwater recharge is required to understand the changes in the temporal water budget and groundwater flow system. The rate of groundwater recharge varies widely in space and time particularly in arid to semiarid regions, and it is rather difficult to measure recharge directly. The aim of this study was to assess the natural groundwater recharge in Al Zerba catchment and the interaction between the surface and groundwater. The catchment is classified as an arid to semiarid climate with an aridity index of 0.25 to 0.3 and long-term average annual precipitation ranging from 300 to 350 mm. Delineation of the catchment boundary was carried out using spatial interpolation of elevation data extracted from the digital elevation model. The effects of vegetation and abstraction from pumping wells on the groundwater table were investigated. Furthermore, groundwater recharge was estimated based on water budget, water table fluctuation analysis by using rainfall infiltration breakthrough, and soil water balance using hydrologic evaluation of landfill performance model (HELP3). The results show that groundwater pumping leads negative impact to long-term decrease in groundwater levels, particularly in the dry season, while no significant effects of vegetation on groundwater were observed. Moreover, the result showed an average annual groundwater recharge ranging from 20 to 35 mm/a (about 10 to 15 % of the precipitation period 2001–2010), concentrated in the north and southwestern regions (outcrops of permeable/coarse-grained limestone and a major fault zone).