Study regionThe Lancang-Mekong River (LMR) in Southeast Asia. Study focusThe LMR provides unparalleled economic and ecological resources for six Asian countries. However, the intensified impact of human activities, coupled with the effects of climate change, has led to alterations in its natural flow, thereby disrupting the river's flow regime. Ensuring the future sustainable management and downstream ecological integrity of this transboundary river requires understanding the regional contributions to the river's altered flow at the sub-basin level. We conducted an analysis for the last four decades using a hydrological model, which divided the entire basin into eight sub-basins, each associated with one of the eight main hydrological stations. New hydrological insights for the regionOur analysis showed significant regional differences in precipitation variation across the LMR, from its headwaters to the lower regions, during both periods. Furthermore, a spatial variation was observed for the impacts of human activities on the natural runoff in both seasons, indicating a lack of effective coordinated management efforts among riparian countries. Notably, our findings indicated that agricultural expansion and the construction of tributary dams in certain sub-basins had a more significant impact on the reduction of the mainstream flow compared to the mainstream dams. These findings underscore the enormous potential of regional water governance to alleviate the impacts of changing climate, offering valuable insights for addressing this critical issue.