Water flow and solute transport through a fractured vadose zone underneath an industrial contaminated site in Belgium were studied with a new methodological concept. The Vadose Zone Experimental Setup (VZES) combines a vadose zone monitoring system (VMS) with cross-borehole geophysics. The VMS provides continuous chemical and hydraulic information at multiple depths in the vadose zone. When combining such information with multidirectional subsurface imaging from geophysical measurements, flow and transport can be characterized at a scale that covers the spatial variability of the subsurface. The setup was installed on site and monitoring was carried out under natural recharge conditions. Results reveal quick rises in water content as a response to rainfall events in the upper and intermediate part of the vadose zone (down to 3.65 m depth). Macropore, micropore, matrix and preferential flow mechanisms are identified at these depth ranges. At greater depths, flow dynamics is slower and dominated by matrix flow. The governance of water flow mechanisms at different directions is controlled by the heterogeneous distribution of geological materials. Results from sampled waters across the vadose zone reveal that the chemistry of water collected from matrix is different from that collected from fractures. In addition, analysis of heavy metals indicates that Ni is leaching across the vadose zone, and its release might be a consequence of pyrite oxidation from backfilled materials. Results obtained from VZES indicate that the combination of different techniques providing in situ quantitative and qualitative information improves conceptual models of flow and transport in a heterogeneous subsurface.