A groundwater flow model of the Alpine valley aquifer in the Aosta Plain (NW Italy) showed that well pumping can induce river streamflow depletions as a function of well location. Analysis of the water budget showed that ∼80% of the water pumped during 2 years by a selected well in the downstream area comes from the baseflow of the main river discharge. Alluvial aquifers hosted in Alpine valleys fall within a particular hydrogeological context where groundwater/surface-water relationships change from upstream to downstream as well as seasonally. A transient groundwater model using MODFLOW2005 and the Streamflow-Routing (SFR2) Package is here presented, aimed at investigating water exchanges between the main regional river (Dora Baltea River, a left-hand tributary of the Po River), its tributaries and the underlying shallow aquifer, which is affected by seasonal oscillations. The three-dimensional distribution of the hydraulic conductivity of the aquifer was obtained by means of a specific coding system within the database TANGRAM. Both head and flux targets were used to perform the model calibration using PEST. Results showed that the fluctuations of the water table play an important role in groundwater/surface-water interconnections. In upstream areas, groundwater is recharged by water leaking through the riverbed and the well abstraction component of the water budget changes as a function of the hydraulic conditions of the aquifer. In downstream areas, groundwater is drained by the river and most of the water pumped by wells comes from the base flow component of the river discharge.