The hyporheic and riparian zones are critical domains in a river ecosystem since they mediate the interactions between surface water and groundwater. These domains are generally strongly heterogeneous and difficult to access; yet their characterization and monitoring still rely mostly on hard-to-perform invasive surveys that provide only point information. These well-known issues, however, can be overcome thanks to the application of minimally invasive methods. In this paper, we present the results of the hydrogeophysical characterization of the Vermigliana Creek's hyporheic and riparian zones, performed at an experimental site in the Adige catchment, northern Italy, by means of electrical resistivity tomography (ERT), distributed temperature sensing (DTS), and hydrological modeling. A major advancement is given by the placement of electrodes and of an optical fiber in horizontal boreholes at some depth below the river bed, put in place via directional drilling. The results of this static and dynamic (time-lapse) geophysical characterization identify the presence of two subdomains (the sub-riverbed and the left and right banks) and define the water flow and solute dynamics. The ERT information is then used, together with other hydrological data, to build a 3D subsurface hydrological model (driven mainly by the watercourse stage variations) that is calibrated against local piezometric information. A solute transport model is then developed to reproduce the variations observed in the dynamic geophysical monitoring. The results show good agreement between ERT data and the model outcome. In addition, the transport model is also consistent with the temperature data derived from DTS, even though some slight discrepancies show that the heat capacity of the solid matrix and heat conduction cannot be totally neglected.