Quebec City’s main drinking water intake is supplied by the 350 km² catchment that feeds the Saint-Charles River. During intensive low flow periods up to 95% of the river discharge is pumped and a strong understanding of surface–subsurface flow interactions is essential to evaluate transient water availability. A fully integrated 3D surface–subsurface flow model of the catchment was developed using the HydroGeoSphere platform to evaluate current and project future transient water availability. This tool and associated results support the stakeholder’s assessment of the vulnerability of Quebec City’s drinking water sources. The 3D surface–subsurface flow model was calibrated using time series of groundwater levels and stream discharges collected from 30 monitoring wells and 15 gauging stations across the catchment. This integrated approach provides a detailed representation of the water cycle and the contribution of groundwater to streamflow. A hydraulic mixing-cell (HMC) post-processing tool was then applied to quantify the fractions of different streamflow components. A modified HMC was then used to estimate water age which enabled the development of innovative vulnerability indices. The results reveal a strong predominance of groundwater at the drinking water intake and an average age of four years. These findings are consistent with isotopic analyses. Future drinking water vulnerability was then assessed by applying climate change and urbanization scenarios to the HMC approach. These simulations provide valuable insights for sustainable water resource management and support the development of robust adaptation strategies for Quebec City.