The hydraulic conductivity of an unconfined carbonate aquifer at the uplifted atoll of Minami-Daito, Japan, was evaluated by a combination of cross-spectral analysis, analytical solution, and density-dependent groundwater modeling based on observed groundwater levels in 15 wells and at sea level. The island area was divided into 10 subregions based on island morphology and on inland propagation of ocean tides. The hydraulic conductivity was obtained for each subregion using analytical solutions based on phase lags of M₂ constituents of ocean tides at each well by assuming two aquifer thicknesses (300 and 1,800 m) and two effective porosities (0.1 and 0.3). The density-dependent groundwater model evaluated the hydraulic conductivity of the subregions by reproducing observed groundwater levels. The hydraulic conductivity in the subregions was estimated as 3.46?×?10^?3 to 6.35?×?10^?2 m/s for aquifer thickness of 300 m and effective porosity of 0.1, and as 1.73?×?10^?3 to 3.17?×?10^?2 m/s for aquifer thickness of 1,800 m and the effective porosity of 0.3. It was higher in southern and northern areas, and higher in interior lowland than in the western and eastern areas. Fissures and dolomite distributions on the island control differences of the omnidirectional ocean tidal propagation and cause these differences in hydraulic conductivity. The method used for this study may also be applicable to other small islands that have few or no data for hydraulic conductivity.