Constraining the magnitude of past hydrological change may improve understanding and predictions of future shifts in water availability. Here we demonstrate that water-table depth, a sensitive indicator of hydroclimate, can be quantitatively reconstructed using Kr and Xe isotopes in groundwater. We present the first-ever measurements of these dissolved noble gas isotopes in groundwater at high precision (≤0.005‰ amu-1; 1σ), which reveal depth-proportional signals set by gravitational settling in soil air at the time of recharge. Analyses of California groundwater successfully reproduce modern groundwater levels and indicate a 17.9 ± 1.3 m (±1 SE) decline in water-table depth in Southern California during the last deglaciation. This hydroclimatic transition from the wetter glacial period to more arid Holocene accompanies a surface warming of 6.2 ± 0.6 °C (±1 SE). This new hydroclimate proxy builds upon an existing paleo-temperature application of noble gases and may identify regions prone to future hydrological change.