California's millennium drought of 2012–2015 severely impacted the Central Valley aquifer system and caused permanent loss of groundwater and aquifer storage capacity. To quantify these impacts within the southern San Joaquin Valley, we analyze various complementary measurements, including gravity changes from Gravity Recovery and Climate Experiment (GRACE) satellites; vertical land motion from Global Positioning System, interferometric synthetic aperture radar, and extensometer; and groundwater level records. The interferometric data set acquired by the Sentinel‐1 satellite only spans the period January 2015 and October 2017, while the other data sets span the entire drought period. Using GRACE observations, we find an average groundwater loss of 6.1 ± 2.3 km3/year as a lower bound estimate for the San Joaquin Valley, amounting to a total volume of 24.2 ± 9.3 km3 lost during the period October 2011 to September 2015. This is consistent with the total volume of 29.25 ± 8.7 km3, estimated using only Global Positioning System deformation data. Our results highlight the advantage of using vertical land motion data to evaluate groundwater loss and thus fill the gaps between GRACE and GRACE‐Follow‐On missions and complement their estimates. We further determine that 0.4–3.25% of the aquifer system storage capacity is permanently lost during this drought period. Comparing groundwater level and vertical land motion data following September 2015, we determine an equilibration time of 0.5–1.5 years for groundwater levels within aquitard and aquifer units, during which residual compaction of aquitard and land subsidence continues beyond the drought period. We suggest that such studies can advance the knowledge of evolving groundwater resources, enabling managers and decision makers to better assess water demand and supply during and in‐between drought periods.