To better understand the changes in the hydrologic cycle caused by global warming in Antarctica, it is crucial to improve our understanding of the groundwater flow system, which has received less attention despite its significance. Both hydraulic and thermal properties of the active layer, through which groundwater can flow during thawing seasons, are essential to quantify the groundwater flow system. However, there has been insufficient information on the Antarctic active layer. The goal of this study was to estimate the hydraulic and thermal properties of Antarctic soils through laboratory column experiments and inverse modeling. The column experiments were conducted with sediments collected from two lakes in the Barton Peninsula, Antarctica. A sand column was also operated for comparison. Inverse modeling using HydroGeoSphere (HGS) combined with Parameter ESTimation (PEST) was performed with data collected from the column experiments, including permeameter tests, saturation-drain tests, and freeze-thaw tests. Hydraulic parameters (i.e., Ks, θs, Swr, α, β, and Ss) and thermal diffusivity (D) of the soils were derived from water retention curves and temperature curves with depth, respectively. The hydraulic properties of the Antarctic soil samples, estimated through inverse modeling, were 1.6 × 10−5–3.4 × 10−4 cm s−1 for Ks, 0.37–0.42 for θs, 6.62 × 10−3–1.05 × 10−2 for Swr, 0.53–0.58 cm−1 for α, 5.75–7.96 for β, and 5.11 × 10−5–9.02 × 10−5 cm−1 for Ss. The thermal diffusivities for the soils were estimated to be 0.65–4.64 cm2 min−1. The soil hydraulic and thermal properties reflected the physical and ecological characteristics of their lake environments. The results of this study can provide a basis for groundwater-surface water interaction in polar regions, which is governed by variably-saturated flow and freeze-thaw processes.