Under the combined influence of climate change and human activities, analysing and predicting water and sediment dynamics is essential for watershed management. This study investigates the Tao River Basin (TRB) on the Tibetan Plateau and the Zuli River Basin (ZRB) on the Loess Plateau-both major tributaries of the upper Yellow River with distinct eco-geographical features. Using the SWAT model to simulate runoff and sediment processes, and partial least squares structural equation modelling (PLS-SEM) to quantify driving mechanisms, we compared how these basins respond to future climate and land use changes. SWAT parameter comparisons revealed that TRB processes are more influenced by vegetation cover and baseflow, whereas ZRB processes are more sensitive to soil properties, moisture transport and channel erosion. PLS-SEM results showed that in the TRB, runoff is mainly driven by precipitation (positive effect) and temperature (suppressive effect), with the positive role of NDVI increasing over time. Sediment dynamics are predominantly controlled by precipitation, with its indirect effects (via NDVI and runoff) outweighing direct meteorological impacts. In the ZRB, runoff is the primary driver of sediment, while precipitation influences both runoff and sediment mainly through vegetation. Temperature has little effect on sediment, and vegetation consistently reduces sediment yield. Scenario analyses indicated distinct trends. Under the low-emission scenario combined with ecological-economic land use, both runoff and sediment are projected to decrease. In contrast, under medium- and high-emission scenarios, both are projected to increase. Notably, the TRB, with its superior vegetation cover, exhibited significantly smaller fluctuations in runoff and sediment across all scenarios. This highlights the key buffering role of vegetation against climate impacts. Therefore, forest and grassland restoration can mitigate climate effects on water and sediment processes. However, sediment control measures may also reduce river runoff, underscoring the need to sustain runoff resources while balancing ecological and socio-economic water needs.