Based on 30 sampling campaigns on precipitation, river water and groundwater in Qingbaijiang urban catchment, southwest China, this study reports the spatio-temporal evolution of water isotopes under the impacts of human activities. The seasonal variation of groundwater-surface water interaction is quantitatively evaluated by isotope-aid hydrograph separation, and the young water fraction (Fyw) in river water at different spatial locations is estimated based on the seasonal periodicity of isotopes. The results show that the stable isotopes in river water and groundwater in Qingbaijiang urban catchment grow enriched from upstream to downstream, reflecting the transformation of the dominant water source from plateau river water to local precipitation and the influence of evaporation. The operation of water conservancy projects and construction of impervious surface in urban areas increase the evaporation intensity of river water. The results of the end-member mixing analysis (EMMA) demonstrates that the average annual contributions of river water to near-bank groundwater are 60.17%, 23.55% and 24.90% in the upper, middle and lower parts, respectively. The periodic storage and release of water led by the water conservancy projects enhances the groundwater recharge in the upstream river, while the water exchanges between river water and groundwater in the middle and lower parts of the catchment are reduced. The Fyw at 8 river sections of Qingbaijiang River estimated by the isotopic amplitude ratio method ranges from 0.067 to 0.194, with an overall increasing trend from upstream to downstream. The young water fraction is negatively correlated with mean elevation, mean slope and vegetation coverage, while positively correlated with the proportion of anthropogenic land use and the proportion of low-permeable soil. The construction of impervious surfaces and drainage systems in urban and rural areas is an important driver for the elevated young water fraction.