Groundwater Dynamics and Aquifer–Stream Interactions in California’s San Joaquin River Basin: Insights from a Coupled SWAT+ Gwflow Framework

Quantifying groundwater depletion and aquifer–stream interactions in intensively irrigated basins remains a critical challenge for sustainable water management. This study numerically examines these issues in the San Joaquin River Basin (SJRB) using the coupled SWAT+ gwflow framework. To manage computational demands across the 28,435 km2 basin, upland contributing areas were represented as inlet point sources at five gauging stations at the outlets of each of the upstream subbasins, reducing computational cost by ~45% while preserving hydrological fidelity. A fine-resolution (300 m × 300 m) model was developed for the downstream valley floor, with release from reservoirs and mountain-block runoff incorporated as a surface boundary condition. We applied the water allocation module gwflow to withdraw water from the aquifer to satisfy crop water stress based on user-defined crop water coefficient values and compared the simulated and observed spatially distributed groundwater head values. Results show a persistent decline in groundwater storage and water levels from 2006 to 2022, with extraction exceeding recharge by ~40%, resulting in an average annual storage loss of 450,175 acre-feet. Intensive pumping also caused hydraulic disconnection between groundwater and some streams, where pronounced cones of depression developed in Turlock, Merced, and western Madera subregions. These findings indicate that targeted managed aquifer recharge and reductions in groundwater extraction in the most severely depleted subregions, are essential to restore aquifer–stream connectivity and ensure long-term water security in the SJRB. Overall, integrating gwflow with SWAT+ provides critical insights into groundwater dynamics in California’s Central Valley and supports sustainable groundwater management.