The microstructure of realistic fluid–rock systems evolves to minimize the overall interfacial energy, enabling local variations in fluid geometry beyond ideal models. Consequently, the permeability–porosity relationship and fluid distribution in these systems may deviate from theoretical expectations. Here, we aimed to better understand the permeability development and fluid retention in deep-seated rocks at low fluid fractions by using a combined approach of high-resolution synchrotron radiation X-ray computed microtomography imaging of synthesized rocks and numerical permeability computation. We first synthesized quartzite using a piston-cylinder apparatus at different fluid fractions and wetting properties (wetting and non-wetting systems with dihedral angles of 52° and 61°–71°, respectively) under conditions of efficient grain growth. Although all fluids should be connected along grain edges and tubules in the homogeneous isotropic wetting fluid–rock system enabling segregation by gravitational compaction in natural settings, the fluid connectivity rapidly decreased to ~ 0 when the total fluid fraction decreased to 0.030–0.037, as the non-ideality of quartzite, including the interfacial energy anisotropy (i.e., grain faceting), became critical. In non-wetting systems, where the minimum energy fluid fraction based solely on the dihedral angle is ~ 0.015–0.035, the isolated (disconnected) fractions was 0.048–0.062. A streamline computation in the non-wetting system revealed that with decreasing total porosity, flow focusing into fewer channels maintained permeability, allowing the effective segregation of the connected fluids. These results provide insight into how non-wetting fluids segregate from rocks and exemplify the fraction of retained fluids in non-wetting systems. Thus, the findings suggest a potential way for wetting system fluids to be transported into the deep Earth's interior, and the amount of fluids dragged down to the Earth’s interior could be higher than what was previously estimated.
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