In recent decades, the hydrological processes on the Loess Plateau have undergone significant changes due to the combined effects of climate change and human activities. This study investigates the Qin River basin, the core area of the Loess Plateau. Between 1971 and 2000, the hydrometeorology of the flood season in the Qin basin on the Loess Plateau in China changed abruptly in 1982 and 1992. This study uses distributed hydrologic modeling and statistical analysis to distinguish the spatial and temporal impacts of climate change and human activities. The fastest dynamic changes in land use occurred in grassland and construction land, accounting for 0.36% and −0.1%, respectively, from 1982 to 1991. From 1992 to 2000, it was 0.29% and 0.3%, respectively. The increase in basin area where the Normalized Difference Vegetation Index increased was 95%. However, except for significant changes in runoff from 1981 to 1992, there were no significant changes in precipitation, runoff, and temperature during other flood seasons. During the two studied variation periods, from 1982 to 1991 and from 1992 to 2000, the contribution rate of climate change to flood season runoff (CClimate) decreased from 83.26% to 74.47%, while the contribution rate of human activity disturbance to flood season runoff (Chuman) increased from 16.74% to 25.53%. In terms of spatial distribution, from 1982 to 1991, areas with a Chuman > 50% were primarily concentrated in the upper reaches of the basin, while from 1992–2000, these areas shifted to the lower reaches. This study offers valuable insights for water resource planning and soil conservation measures in the Loess Plateau and similar arid regions worldwide, aiming to ensure water resource safety and sustainability in response to climate change and human interference.