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Understanding groundwater flow in heterogeneous alluvial aquifers is essential for sustainable water resource management and preserving riparian ecosystems, particularly in mountainous regions where surface–subsurface interactions play a critical role. This study investigates the hydrological functioning of the R¨othenbach alluvial aquifer (Emmental, Switzerland), a dynamic pre-Alpine groundwater system. Using historical data from the 1986 Blue Report and new geological interpretations, 2D and 3D steady-state hydrogeological models was developed using MODFLOW. A sensitivity analysis of model outputs (hydraulic head, groundwater outflow, and river–aquifer exchange fluxes) was conducted across a broad range of hydraulic conductivity and streambed conductance values. Homogeneous models showed that while average groundwater behavior can be reproduced, they are not able to replicate local variability observed in the field. To better reflect subsurface heterogeneity, a series of stochastic geological models were generated using Multiple Point Statistics (MPS) based on limited borehole data and directional constraints tied to valley orientations to reproduce deposition structures Results show that even when mean properties are held constant, variations in low-permeability lenses placement can lead to substantial differences in modeled hydraulic heads and stream–aquifer interactions. This highlights the importance of hydraulic properties heterogeneity in controlling local groundwater dynamics. The approach demonstrates the potential of MPS-based modeling to improve the representation of geological heterogeneity in data-scarce environments and provides a foundation for future transient simulations incorporating time-series data.