The Yellow River Basin (YRB) faces escalating pressures from climate variability and intensive land-use change; however, how these drivers jointly shape the water ecosystem services (WES) remains insufficiently quantified. This study assessed water yield, soil conservation, and water purification capacity across the YRB from 2000 to 2020 using the InVEST model. The effects of driving forces, including climate and land-use changes, on WES were examined using scenario simulation and the geographical detector method. During 2000–2020, water yield and soil conservation displayed fluctuating upward trends, increasing by 26.24% and 30.19%, respectively, whereas nitrogen and phosphorus exports declined slightly by 4.82% and 3.08%, indicating a modest improvement in water purification. All indicators exhibited elevated values in the southeast and lower values in the northwest, with clear distinctions among the three topographic zones. The contribution rates of climate change to variations in water yield, soil conservation, nitrogen export, and phosphorus export were 97.4–99.3, 94.5–98.3, 87.2–96.0, and 85.7–95.2%, respectively, indicating the central regulatory role of climatic factors in watershed-scale water-related ecological processes. However, the contribution of land-use factors increased over time and had a significantly greater impact on water purification capacity. Distinct spatial heterogeneity was observed among the WES. Interactions among climatic, topographic, and other factors significantly enhanced the spatial variability of water yield and soil conservation services, while land-use interactions with other drivers had greater impacts on the spatial variability of water purification capacity. Thus, regionally differentiated policy strategies are essential. Our findings provide a quantitative basis for differentiating climate versus land-use interventions in water resource management and designing spatially targeted ecological restoration policies in the YRB and similar regions worldwide.