Climate changes and other human activities have substantially altered the hydrological cycle with respect to elevation. In this study, longitudinal patterns in the stable isotopic composition (δ2H and δ18O) of Lancang River water, originating from the Qinghai–Tibetan Plateau, are presented, and several controlling factors in the wet season are hypothesized. Lancang River water δ2H (−145.2‰ to −60.7‰) and δ18O (−18.51‰ to −8.49‰) were low but close to those of the Global Meteoric Water Line. In the upper reaches of the river, δ2H decreased longitudinally, potentially due to groundwater inputs and melting ground ice in the headwater zone and to an increasing proportion of glacier meltwater with decreasing elevation. In the middle reaches of the river, δ2H values increased slowly moving downstream, likely due to shifts in precipitation inputs, as evidenced by the isotopic composition of tributaries to the main stream. In the lower reaches of the river, the isotopic composition was relatively invariant, potentially related to the presence of large artificial reservoirs that increase the water resident time. The results reveal different hydrological patterns along an alpine river in central Asia associated with both natural and anthropogenic processes. Understanding the degree and type of human interference with the water cycle in this region could improve water management and water security.