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We estimated potential changes in annual, seasonal, and high and low runoff and associated uncertainty in the 218 sub-basins of the Willamette River basin of Oregon for the 2040s and the 2080s. The US Geological Survey’s Precipitation–Runoff Modeling System (PRMS) was calibrated and validated for representative river basins between 1973 and 2006. A regionalization method and GIS analysis determined the PRMS model parameters for ungauged basins. We used a combination of eight general circulation models (GCMs) and two emission scenarios downscaled to 1/16° resolution to estimate spatial and temporal changes in future runoff at a sub-basin scale. The seasonal variability of runoff is projected to increase consistently with increases in winter flow and decreases in summer flow. These trends are amplified under the A1B emission scenario by the end of the 21st century with increases in top 5% flow …