Global climate change will likely increase temperature and variation in precipitation in the Himalayas, modifying both supply of and demand for water. This study assesses combined impacts of land-cover and climate changes on hydrological processes and a rainfall-to-streamflow buffer indicator of watershed function using the Soil Water Assessment Tool (SWAT) in Kejie watershed in the eastern Himalayas. The Hadley Centre Coupled Model Version 3 (HadCM3) was used for two Intergovernmental Panel on Climate Change (IPCC) emission scenarios (A2 and B2), for 2010–2099. Four land-cover change scenarios increase forest, grassland, crops, or urban land use, respectively, reducing degraded land. The SWAT model predicted that downstream water resources will decrease in the short term but increase in the long term. Afforestation and expansion in cropland will probably increase actual evapotranspiration (ET) and reduce annual streamflow but will also, through increased infiltration, reduce the overland flow component of streamflow and increase groundwater release. An expansion in grassland will decrease actual ET, increase annual streamflow and groundwater release, while decreasing overland flow. Urbanization will result in increases in streamflow and overland flow and reductions in groundwater release and actual ET. Land-cover change dominated over effects on streamflow of climate change in the short and middle terms. The predicted changes in buffer indicator for land-use plus climate-change scenarios reach up to 50% of the current (and future) range of inter-annual variability.