The evaluation and quantification of aquifer structure in the Earth Critical Zones (CZ) are of great significance to the hydrological cycle and water resources management. 【Objective】 However, the characterization of complex CZ structures at spatial scales remains a huge challenge. In this paper, research was conducted on a small karst dolomite watershed (1.20 km²) in northwest Guangxi province, China, to quantify the distribution characteristics of aquifer media in CZ and analyze its influencing factors. 【Method】 a total of 21 electrical resistivity tomography survey lines with a total length of 12, 605 meters was set up and combined with hydrological drilling at the watershed scale. 【Result】 The results show that tectonic movement and dynamic metamorphism resulted in the development of multiple fault zones in the small watershed. This provided the material and dynamic basis for the spatial distribution of karst water-bearing media (including soil, surface karst zone, and surface karst spring). The fault zone was concentrated in the depression, which has a good hydrodynamic and dissolution environment. As a result, the soil and epikarst thickness in the depression was higher than that in hillslope, and there was a significant (P < 0.05) negative linear relationship with elevation. Besides, the spatial coupling degree of soil and epikarst thickness was high, showing a significant positive linear relationship (R² = 0.63, P < 0.01) between soil and epikarst thickness. It was related to slope erosion and confluence, and special water-CO₂-rock interaction in the soil-epikarst zone system. Karst aquifer flows out of the depression or down hillslope, and its hydrological characteristics were related to the distribution and water storage features of the soil-epikarst system. 【Conclusion】 This study provides data and technical support for the characterization of the karst aquifer at the catchment scale and construction of the land surface model in future studies.