The hyporheic zone (HZ) is a critical area of all river ecosystems. It is the area beneath the stream and adjacent to the stream, where the surface water and groundwater are mixed. The HZ extends both vertically and laterally depending on the sediment configuration, namely their porosity and permeability. This influences the hyporheic communities’ structural pattern and their active dispersal among distinct rivers compartments and alluvial aquifers. It is still difficult to assess the spatial extent of the HZ and the distribution of the mixing zones. This study applies time-lapse images obtained using electrical resistivity tomography (ERT) of 20 m wide and 5 m deep alluvial streams, with regards to the structural pattern of hyporheic communities represented by cyclopoids and ostracods, in order to assess the extent of the HZ in the riverbed and the parafluvial sediment configurations. The ERT images obtained at the hyporheic Site 1 are characterized by alluvial deposits dominated by coarse and very coarse sands with resistivity values ranging from ~20 to 80 Ohm.m, indicating a permeable zone up to ~0.5 m thick and extending laterally for ca. 5 m from the channel and associated with the hyporheic zone. The sediment configurations, texture, and structure indicate an active surface–hyporheic water exchange and low water retention into the sediments. This is also indicated by the hyporheic copepods and ostracods communities’ structure formed by a mixture of non-stygobites (five species) and stygobites (two species). A low-resistivity (<70 Ohm.m) permeable zone located 2.3 m below the streambed and unconnected with the river channel was also detected and associated with the associated alluvial aquifer. In contrast, the resistivity image at Site 2 dominated by coarse, medium, and very fine sands, shows a low-permeability zone in the upper ~0.5 m of the profile, with a resistivity value ranging from ~45 to 80 Ohm.m, indicating a reduced HZ extension in both vertical and lateral dimensions. Here the sediment configurations indicate that the water retention and interaction with the sediment is higher, reflected by more diverse hyporheic communities and with highly abundant stygobite species. The two examples show that non-invasive ERT images and biological assessments provide complementary and valuable information about the characterization of the sub-channel architecture and its potential hydraulic connection to the floodplain aquifer.