<p>In Japan, subsurface dams have been constructed to artificially recharge natural aquifers, which primarily comprise the strata of Quaternary Ryukyu limestone. The high porosity of the Ryukyu limestone makes it an excellent reservoir; however, its flow characteristics remain uncertain. In this study, we used X-ray computed tomography (CT) and pore-scale modeling to evaluate the pore and flow characteristics of the Ryukyu limestone samples. The CT results revealed a positive correlation between the porosity and connection probability (i.e., degree of connectivity between pores); the coefficient of variation of the porosity in the vertical direction tended to be smaller when the porosity of the entire region of interest was large. The pore-scale models showed that the flow was concentrated in a few channels (i.e., highly heterogeneous) and that the hydraulic conductivity and its anisotropy were highly dependent on the pore structure in the region of interest. These results enhance our understanding of pore structure and hydraulic behavior in Ryukyu limestone and provide a foundation for future assessments of groundwater flow and contaminant transport in subsurface dam reservoirs.</p>