Quantifying the potential impacts of climate change on water yield and ecosystem productivity is essential to developing sound watershed restoration plans, and ecosystem adaptation and mitigation strategies. This study links an ecohydrological model (Water Supply and Stress Index, WaSSI) with WRF (Weather Research and Forecasting Model) using dynamically downscaled climate data of the HadCM3 model under the IPCC SRES A2 emission scenario. We evaluated the future (2031-2060) changes in evapotranspiration (ET), water yield (Q) and gross primary productivity (GPP) from the baseline period of 1979-2007 across the 82 773 watersheds (12-digit Hydrologic Unit Code level) in the coterminous US (CONUS). Across the CONUS, the future multi-year means show increases in annual precipitation (P) of 45mmyr-1 (6 %), 1.8° C increase in temperature (T), 37mmyr-1 (7 %) increase in ET, 9mmyr-1 (3 %) increase in Q, and 106 gCm-2 yr-1 (9 %) increase in GPP. We found a large spatial variability in response to climate change across the CONUS 12-digit HUC watersheds, but in general, the majority would see consistent increases all variables evaluated. Over half of the watersheds, mostly found in the northeast and the southern part of the southwest, would see an increase in annual Q (> 100mmyr-1 or 20 %). In addition, we also evaluated the future annual and monthly changes of hydrology and ecosystem productivity for the 18 Water Resource Regions (WRRs) or two-digit HUCs. The study provides an integrated method and example for comprehensive assessment of the potential impacts of climate change on watershed water balances and ecosystem productivity at high spatial and temporal resolutions. Results may be useful for policy-makers and land managers to formulate appropriate watershed-specific strategies for sustaining water and carbon sources in the face of climate change.