Human activities and climate are two key factors affecting hydrological and soil erosion processes. Understanding their impacts on water discharge and sediment transport is very important for sustainable development of watersheds, particularly in subtropical regions with high precipitation and high sediment loads. We here compared the long-term dynamics of water discharge and sediment transport in four large contiguous watersheds in subtropical China and explored the importance of the main influencing factors including climate, nature endowment such as geology, and human activities. Significant differences have been observed between watersheds in terms of sediment and water discharge (p < 0.001). Pairwise comparison among the four basins demonstrated significant differences in sediment modulus among 5 of the 6 pairs (p < 0.05). The sediment modulus in the Lishui Basin was significantly higher than those in other basins, mainly due to the substantial presence of steep slopes in the mountainous region, which is prone to soil erosion. Temporally, sediment transport in the four basins was well synchronized showing significant decreasing trends with abrupt change points (p < 0.001). In contrast, no trends and abrupt change points were detected in water discharge, mainly influenced by precipitation. Human activities played a predominant role to the reduction of sediment transport (80% to 102%) compared with those of climate (-2% to 19%) across the four basins. Additionally, our study also showed land cover had various basin-independent impacts on the change of sediment transport. Through cross-basin comparisons of the long-term changes in water discharge and sediment transport, our study revealed the similarities and differences in their driving mechanisms, providing valuable information for land use planning and water resource management in large subtropical basins.