Fractured rock aquifers are susceptible to contamination, with metal(loid)s rapidly migrating from poorly developed overburden to the fractured rock vadose zone and thus into groundwater. Compared to typical porous aquifers, retention effects within the rock matrix are small, and rapid advection along fractures leads to a higher risk of groundwater contamination. However, the highly complex anisotropic pathways of natural fractures hinder research in this field. To construct reproducible fractures, this study used 3D printing following Computed X-ray Microtomography (μCT) scans of a fractured rock collected in a natural limestone aquifer. Stimulated metalloid release was observed in the fractured rock during column leaching, and the leachate concentrations of arsenic (As) and antimony (Sb) increased by up to 17.5 and 36.4 times, respectively, compared with the porous vadose zone. Fluctuations in fracture metalloid release patterns in dissolved and adsorbed phases were attributed to retention and filtration effects induced by soil particles within fractures. Geophysical properties of the porous overburden, especially the aggregation characteristics, greatly affected the non-equilibrium leaching behavior of As, but had a limited effect on the near-equilibrium leaching of Sb, which was explored by modifying the surficial soil layer with either montmorillonite clay or charcoal. The results of this study provide a novel method and useful information for modeling and risk assessment of fractured rock aquifers.