Understanding the factors controlling groundwater recharge in arid vadose zones is critical for sustainable groundwater management in the face of climate variability and change. Here we estimated groundwater recharge in data sparse regions under arid climate by implementing a multi-model approach using HYDRUS-1D for a century-long time series of meteorological data and site-specific regolith hydraulic properties of a bare soil and a Mulga savanna-type soil in central Australia. Grain‐size analysis provided a contiguous 12-m deep profile of hydraulic properties that were generated by means of pedotransfer functions. To account for conceptual model uncertainty in hydraulic properties, eleven pedotransfer functions were applied. Climate data from three stations accounted for spatial heterogeneity in local climate of the Ti Tree Basin study area. Simulated water fluxes in the vadose zone indicated that only rainfall events of more than 150–200 mm resulted in groundwater recharge. Recharge was linked to extreme rainfall associated with monsoonal cyclones. Based on the 130-year climate record, average recharge for the savanna-type vegetation ranged from 4.3 to 7.4 mm/a across the three climate stations, with an overall mean of 4.6 mm/a. The bare soil had an overall mean recharge of 29.5 mm/a, ranging from 23.5 to 35.8 mm/a. Results from this study provide a better understanding of the highly episodic recharge in arid environments and are critical input to sustainably manage groundwater resources.