Although evidence of the hydrological response of watersheds to climate change is abundant, reliable assessments of water yield (WY) over mountainous regions, such as the Upper Brahmaputra River (UBR) basin, remain unclear. Here, we examine long-term WY changes during 1982–2013 in the UBR basin, based on multi-station runoff observations. We find that there are significant shifts in hydrological regimes in the late 1990s; WY increases in the range of ∼10 % to ∼80 %, while the directions reverse from increasing to decreasing. Additionally, the double mass curve (DMC) technique is used to assess the effects of climate, vegetation, and cryosphere on WY changes. Results show that cryosphere and climate together contribute to over 80 % of the increase in WY across the entire UBR basin, while the role of vegetation is negligible. The combined effects, however, are either offsetting or additive, thus leading to slight or substantial magnitude increases, respectively. The downward WY trend has primarily been regulated by decreased precipitation in recent years. However, we find that meltwater may alleviate the resulting water shortage in some basins. Therefore, the combined effects of climate and cryosphere on WY should be considered in future water resources management over mountainous basins, particularly involving co-benefits between upstream and downstream regions.