In mountainous river basins, groundwater systems are sustained by complex recharge processes and geological heterogeneity, making groundwater flow simulation challenging in data-scarce regions where hydrological inputs are often assumed to be spatially uniform. This study developed a heterogeneous geological model of the Kofu Basin, Japan, using multiple boreholes and simulated the groundwater flow by integrating MODFLOW with climate-driven recharge outputs from SWAT+. Simulated groundwater flow was evaluated against findings from previous stable isotope studies to assess the plausibility of the simulated recharge system. After calibration, the model performance improved substantially: RMSE decreased by 91.28%, MAE decreased by 84.38%, and NSE increased from 0.9530 to 0.9996. Independent validation showed good regional agreement between observed and simulated groundwater heads (R² = 0.9307; NSE = 0.9254), although RMSE and MAE remained relatively high at 32.70 m and 19.76 m, respectively, suggesting remaining uncertainty in local-scale groundwater head simulation. Simulated velocity vectors indicated localized shallow flow and more coherent regional basinward flow in the deeper aquifer. This pattern is consistent with the interpretation that mountain-derived recharge contributes to the deeper regional groundwater system. The results highlight the value of combining hydrogeological models and geochemical evidence to support recharge-process interpretation in complex mountainous basins.