This paper focuses on quantifying the uncertainty in climate change and its impacts on hydrology in the Srepok watershed in the Central Highlands of Vietnam. The uncertainty associated with the general circulation model (GCM) structure from a subset of CMIP3 (CCCMA CGCM3.1, CSIRO Mk3.0, IPSL CM4, MPI ECHAM5, NCAR CCSM30, UKMO HadGEM1, and UKMO HadCM3), SRES emission scenarios (A1B, A2, B1, and B2), and prescribed increases in global mean temperature (0.5–6 °C) using the soil and water assessment tool (SWAT) was investigated. For prescribed warming scenarios using HadCM3, linear decreases in mean annual streamflow ranged from 2.0 to 9.8 %. Differences in projected annual streamflow between SRES emission scenarios using HadCM3 were small (−3.8 to −3.3 %). Under the A1B scenario and 2 °C increase in global mean temperature using seven GCMs, there was substantial disparity, of −3.7 to 21.0 % and −6.0 to 16.1 %, respectively. It was concluded that, in the case of the Srepok watershed, the most important source of uncertainty comes from the GCM structure rather than from the emission scenarios and climate sensitivity.