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The geometric and spatial heterogeneity in fracture systems of natural fault zones reflect complex strain patterns and exert substantial influences on host rock properties. It has been recognized that general 3D strains will produce diffuse fracture orientation patterns and characteristic kinematics, which are proposed to vary towards the fault core. The bootstrapping methods and spatial correlation analysis [(semi-) variograms] were adopted to investigate the geometric and spatial hetero-geneity in fracture orientations collected systematically with reference to their spatial locations from three distinct fault zones. This relatively rigorous approach revealed that fracture orientation patterns display systematic spatial variations and high spatial correlations traversing fault zones. Factors related to the presence of pre-existing structures and lithologies can modify strains, creating complex fracture patterns and kinematics at different scales and spatial locations. The results suggest that spatially heterogenous fracture networks in subsurface can be highly connected as channels or barriers and will, in anyways, affect the fluid flow path in aquifers.