Aquifers are vital groundwater reservoirs for residential, agricultural, and industrial activities worldwide. Tracking their state with high temporal and spatial resolution is critical for water resource management at the regional scale yet is rarely achieved from a single type of groundwater data. Here we show that variations in groundwater levels can be mapped using perturbations in seismic velocity (dv/v). We measure dv/v in the San Gabriel Valley, California, from cross correlation of the ambient seismic field. dv/v reproduces the groundwater level changes that are marked by the multiyear depletions and rapid recharges, typical of California's cycles of droughts and floods. dv/v correlates spatially with vertical surface displacements and deformation measured with the Global Positioning System (GPS). Our results successfully predict the volume of water lost in the San Gabriel Valley during the 2012–2016 drought and thus provide a new, complementary approach to monitor groundwater storage.