<p>Evaluating rainwater transport patterns is critical to understanding coupled hydrological cycles. However, water movement in heterogeneous landscapes exhibits pronounced complexity, particularly as the impacts of subsurface geotechnical structures remain inadequately understood. We applied water isotope tracers to compare mobile water recharge characteristics in two humid karst hillslopes with distinct soil thicknesses (deep-soil, DSH; shallow-soil, SSH). Mobile water was collected from (<i>i</i>) soil water at multiple depths across downslope-to-upslope positions, and (<i>ii</i>) lateral subsurface runoff within the soil-bedrock system at discharge outlets. The rainwater replenishment proportion (<i>β</i>) and mean transit time (MTT) of soil water, and evaporated fractionation (<i>f</i>) in runoff during consecutive rainless days were used to quantify recharge characteristics. The results showed that the mean <i>β</i> value in SSH was 22.49%, exceeding the 15.07% in DSH. In contrast, the soil and runoff MTT in DSH (−42.41 days) was longer than in SSH (−30.58 days). These findings indicate that SSH mobile water exhibits a higher rainwater recharge ratio but a shorter residence time, which is associated with its stronger water infiltration capacity. As supporting evidence, SSH was more susceptible to evaporation, manifested by a higher <i>f</i> in SSH (13.5%) compared to DSH (9.3%). In DSH, a strong correlation (<i>R</i>²=0.78) between <i>β</i> and MTT was observed, whereas this relationship was weak in SSH (<i>R</i>²=0.16). Therefore, we highlight that the high heterogeneity of shallow soil hillslopes may render infiltration-runoff processes more complex and unpredictable in karst hillslopes in Southwest China.</p>