Understanding the origins of groundwater and its movement from hillslopes to valleys is critical for conserving water supplies, determining water-use policies and controlling pollution. These factors are also the keys for understanding the dominant processes in hydrological models. In this study, the sources of groundwater from hillslopes to valleys were explored by using a multiple-hillside observatory in an agricultural catchment in Southwest China. Stable isotope tracers (e.g., O-18 and H-2) combined with the concept of line-conditioned excess (lc-excess), which describes the offset of the groundwater evaporation line from the local meteoric water line, were used to understand the development of kinetic fractionation at specific sampling sites and to further determine the threshold for precipitation recharge to groundwater. The results showed that the isotope kinetic fractionations of soil water and shallow groundwater in the rainy season were stronger than those in the dry season. The precipitation sources and temperatures were the key factors affecting groundwater isotope fractionation. The recharging processes and the increasing lc-excess values from upslope areas to the valleys indicated a greater contribution of lateral flow from the upslope. In the rainy season, precipitation amounts greater than 30 mm d(-1) could effectively recharge the shallow groundwater in the study area. Our results confirmed that it was possible to elucidate the recharging mechanisms of shallow groundwater by using the dual-isotope method based on the lc-excess concept. It is anticipated that a broader application of these findings could be helpful for evaluating water resource sustainability in the subtropics, particularly in hilly regions.