Surface deformation in California’s Central Valley (CV) has long been linked to changes in groundwater storage. Recent advances in remote sensing have enabled the mapping of CV deformation and associated changes in groundwater resources at increasingly higher spatiotemporal resolution. Here, we use interferometric synthetic aperture radar (InSAR) from the Sentinel-1 missions, augmented by continuous Global Positioning System (cGPS) positioning, to characterize the surface deformation of the San Joaquin Valley (SJV, southern two-thirds of the CV) for consecutive dry (2016) and wet (2017) water years. We separate trends and seasonal oscillations in deformation time series and interpret them in the context of surface and groundwater hydrology. We find that subsidence rates in 2016 (mean −42.0 mm/yr; peak −345 mm/yr) are twice that in 2017 (mean −20.4 mm/yr; peak −177 mm/yr), consistent with increased groundwater pumping in 2016 to offset the loss of surface-water deliveries. Locations of greatest subsidence migrated outwards from the valley axis in the wetter 2017 water year, possibly reflecting a surplus of surface-water supplies in the lowest portions of the SJV. Patterns in the amplitude of seasonal deformation and the timing of peak seasonal uplift reveal entry points and potential pathways for groundwater recharge into the SJV and subsequent groundwater flow within the aquifer. This study provides novel insight into the SJV aquifer system that can be used to constrain groundwater flow and subsidence models, which has relevance to groundwater management in the context of California’s 2014 Sustainable Groundwater Management Act (SGMA).