Time-lapse ground-penetrating radar (GPR) surveys, combined with automated infiltration experiments, provide a non-invasive approach for investigating the distribution of infiltrated water within the soil medium and creating three-dimensional images of the wetting bulb. This study developed and validated an experimental protocol aimed at quantifying and visualizing water distribution fluxes in layered soils under both unsaturated and saturated conditions. The 3D images of the wetting bulb significantly enhanced the interpretation of infiltration data, enabling a detailed analysis of water movement through the layered system. We used the infiltrometer data and the Beerkan Estimation of Soil Transfer parameters (BEST) method to determine soil capacitive indicators and evaluate the physical quality of the upper soil layer. The field survey involved conducting time-lapse GPR surveys alongside infiltration experiments between GPR repetitions. These experiments included both tension and ponding tests, designed to sequentially activate the soil matrix and the full pore network. The results showed that the soil under study exhibited significant soil aeration and macroporosity (represented by AC and pMAC), while indicators related to microporosity (such as PAWC and RFC) were notably low. The RFC value of 0.55 m3 m−3 indicated the soil’s limited capacity to retain water relative to its total pore volume. The PAWC value of 0.10 m3 m−3 indicated a scarcity of micropores ranging from 0.2 to 30 μm in diameter, which typically hold water accessible to plant roots within the total porosity. The saturated soil hydraulic conductivity, Ks, values ranged from 192.2 to 1031.0 mm h−1, with a mean of 424.4 mm h−1, which was 7.9 times higher than the corresponding unsaturated hydraulic conductivity measured at a pressure head of h = −30 mm (K−30). The results indicated that the upper soil layer supports root proliferation and effectively drains excess water to the underlying limestone layer. However, this layer has limited capacity to store and supply water to plant roots and acts as a restrictive barrier, promoting non-uniform downward water movement, as revealed by the 3D GPR images. The observed difference in hydraulic conductivity between the two layers suggests that surface ponding and overland flow are generated through a saturation excess mechanism. Water percolating through the soil can accumulate above the limestone layer, creating a shallow perched water table. During extreme rainfall events, this water table may rise, leading to the complete saturation of the soil profile.