Karst landforms are renowned for their unique characteristics, and investigating karst development characteristics is of great significance for groundwater regulation and ecological management. This study aims to interpret karst distribution under different topographic conditions in a watershed using Electrical Resistivity Tomography (ERT). Taking the Chenqi small watershed in Southwest China as the study area, 10 ERT survey lines were deployed across three topographic settings (dip slopes, anti-dip slopes, and high-lying depressions). By combining 2D/3D ERT inversion, geological drilling, and outcrop verification, the subsurface karst distribution was revealed. The results show that ERT effectively detects karst features with high heterogeneity and discontinuity. Conduit-type karst appears in the middle section of both slopes, indicating groundwater migration pathways. Karst water is dominated by runoff on dip slopes, whereas infiltration dominates on anti-dip slopes; continuous low-resistivity aquicludes in high-lying depressions control local groundwater levels. The average karst zone thickness is 2.0–4.0 m, with a maximum of 12 m. These findings demonstrate a coupled relationship between karst structure and groundwater runoff under topographic differentiation, providing a quantitative reference for watershed-scale groundwater processes and practical value for karst water exploration, resource regulation, and slope stability assessment.