The San Joaquin Valley (SJV) of California is one of the world’s most productive agricultural regions. Reliance on groundwater has led to some of the greatest rates of human-induced land subsidence in the world in the 20th century, as well as more recently. The United States Geological Survey (USGS) has recently developed an integrated surface–subsurface hydrologic model, the Central Valley Hydrologic Model 2 (CVHM2), that represents the major components of the hydrologic system of California’s Central Valley. In this study, CVHM2 was applied as a decision support tool while simulating various management strategies to mitigate the land subsidence caused by the extraction of groundwater. CVHM2 was extended through to 2073 and applied to simulate management scenarios in terms of three primary drivers and their impact on subsidence along the Delta–Mendota Canal (DMC), a critical piece of infrastructure in the western SJV. The drivers considered were agricultural water demands, managed aquifer recharge (MAR), and changes in future climate. The results show that future subsidence is most sensitive to water demands, second most sensitive to future changes in climate, and relatively insensitive to MAR when it is applied as a surface application in the western SJV. However, we demonstrate via proof-of-concept scenarios that the MAR is capable of arresting subsidence when implemented via injection below the Corcoran Clay Member of the Tulare Formation instead of as a surface application. We also examine the uncertainty that is the result of climate variability and how to use the tool to identify the most appropriate strategies to constrain future subsidence to acceptable levels.