Accurate mapping of groundwater vulnerability zones based on robust groundwater model is crucial towards anappropriate development of management strategies. This study aimed at developing groundwater vulnerability zones in a tropical karst area in Rote Island, Indonesia. HGZ method was employed to accommodate the limitation of subsurface data. Using reverse particle-tracking simulation, this study combined the simulation results (travel time and pathline trajectory) with the potential groundwater contamination risk to designate three vulnerability zones. In this study preventive management measures were recommended to ensure provision of safe and good quality water from Oemau Spring and to protect the spring from contamination.