Freshwater resources are at a premium across the world, including many water-limited areas across Australia. Ongoing water level decline in some groundwater systems suggests that the rate of loss may have reached unsustainable levels . However, identifying which factors are primarily responsible for the trend (lack of rainfall-recharge, presence of vegetation, and groundwater pumping) remains challenging using groundwater observations alone. We applied satellite-derived estimates of evapotranspiration (ETa), which, when combined with local rainfall data and field-based groundwater level observations, established a regional water balance spanning 1,500 km(2) and seven groundwater lenses over a 10-year period (2000 - 2010). Assuming that the extent of the freshwater isohaline represents the recharge area for a lens, the water balance suggests that the median annual groundwater recharge rate varied between 226 +/- 92 mm year(-1) (Mikkira) and -162 +/- 194 mm year(-1) (Uley East). Uley South is the most regionally significant lens in the system and recorded a median annual recharge rate of 91 +/- 182 mm year(-1). Overlaying vegetation highlighted the impact of woodland areas on groundwater recharge, where the trees were accessing groundwater to support ETa, provided the water table was <10 m. Areas of grassland demonstrated the highest median groundwater recharge rates of 151 mm year(-1), followed by cropping (133 mm year(-1)) and pasture (95 mm year(-1)). Exploring the resilience of the groundwater system to variations in extraction (pumping) and woodland coverage suggests that resource managers must consider both systematic losses in order to maintain groundwater equilibrium.