Soil water plays an important role in the ecological restoration of karst areas impacted by rocky desertification (KRD) caused by deforestation. A better understanding of the spatiotemporal dynamics and modes of water flow in KRD areas is essential for satisfactory soil water management. This study examines the soil water content (SWC) and stable isotope (δ¹⁸O and δD) patterns in seven sampling sites along an E-W transect in a typical small karst basin in southwest China over the hydrologic year, February, 2018–January, 2019. The results of this study show that the spatial differences of SWC and soil water δ¹⁸O (δD) values were smaller but in with clear seasonal variations. Seasonal vertical profiles of soil water δ¹⁸O (δD) showed a decreasing trend from the surface to a depth of 100 cm in February, April, and June, which reversed August and October. Shallow soil water δ¹⁸O (δD) and line-conditioned excess (lc-excess) (< 20 cm depth) showed significantly stronger seasonality than the deeper soil water (> 20 cm depth). Enriched soil water δ¹⁸O (δD) values in the upper 20 cm depth was closely related to the potential evaporation over the 7 days prior to each sampling (PET₇). Piston flow was the dominant mode of flow in the sampling sites, inferred from the vertical profile characteristics of the soil water δ¹⁸O (δD). The influence of evaporative processes was limited to the upper 20 cm depth of the soil. The fraction of evaporation losses from soil water storage at the 20 cm depth varied from − 15.8% to 12.3%, based on δD estimates, and from − 13.3% to 14.0% based on δ¹⁸O. These results are important for effective soil water management in KRD areas that experience seasonal drought.