Land subsidence, caused by groundwater extraction and subsequent subsurface compaction, is an issue of global concern. Since the 1920s, there have been numerous periods of subsidence in California’s San Joaquin Valley leading to widespread sinking of the land surface which has locally exceeded 9 m. The most recent period of severe subsidence, which was triggered by the 2012-15 drought, is now causing damage which threatens the long-term viability of critical water distribution infrastructure in the Valley. However, there is neither a continuous monitoring record of the subsidence nor high-quality records of the hydrologic head changes in the subsurface which have caused the subsidence, making it impossible to understand, and thus mitigate, the subsidence. Here, we leverage subsidence and hydraulic head data from a variety of sources to create and validate a one-dimensional model of subsurface compaction and subsidence over the 65 years between 1952-2017. This model, which simulated up to 7.5 m of subsidence since 1952, provides a complete record of subsidence in our study region by filling crucial gaps in the observed record. Our model reveals the long-term processes causing subsidence, which operated over decades-to-centuries and caused exceptionally high rates of baseline subsidence in 2017, resulting in a critical risk of future subsidence. This risk is exacerbated as the Valley moves into drought conditions again in Spring 2021. We demonstrated an approach which provided the understanding of subsidence in the Valley needed to directly inform sustainable groundwater management, and which is applicable in subsiding regions around the World.