Downscaling Global Climate Model (GCM) projections of future climate is critical for impact studies. Downscaling enables use of GCM experiments for regional scale impact studies by generating regionally specific forecasts connecting global scale predictions and regional scale dynamics. We employed the Statistical Downscaling Model (SDSM) to downscale 21st century precipitation for two data-sparse hydrologically challenging river basins in South Asia—the Ganges and the Brahmaputra. We used CGCM3.1 by Canadian Center for Climate Modeling and Analysis version 3.1 predictors in downscaling the precipitation. Downscaling was performed on the basis of established relationships between historical Global Summary of Day observed precipitation records from 43 stations and National Center for Environmental Prediction re-analysis large scale atmospheric predictors. Although the selection of predictors was challenging during the set-up of SDSM, they were found to be indicative of important physical forcings in the basins. The precipitation of both basins was largely influenced by geopotential height: the Ganges precipitation was modulated by the U component of the wind and specific humidity at 500 and 1000 h Pa pressure levels; whereas, the Brahmaputra precipitation was modulated by the V component of the wind at 850 and 1000 h Pa pressure levels. The evaluation of the SDSM performance indicated that model accuracy for reproducing precipitation at the monthly scale was acceptable, but at the daily scale the model inadequately simulated some daily extreme precipitation events. Therefore, while the downscaled precipitation may not be the suitable input to analyze future extreme flooding or drought events, it could be adequate for analysis of future freshwater availability. Analysis of the CGCM3.1 downscaled precipitation projection with respect to observed precipitation reveals that the precipitation regime in each basin may be significantly impacted by climate change. Precipitation during and after the monsoon is likely to increase in both basins under the A1B and A2 emission scenarios; whereas, the pre-monsoon precipitation is likely to decrease. Peak monsoon precipitation is likely to shift from July to August, and may impact the livelihoods of large rural populations linked to subsistence agriculture in the basins. Uncertainty analysis of the downscaled precipitation indicated that the uncertainty in the downscaled precipitation was less than the uncertainty in the original CGCM3.1 precipitation; hence, the CGCM3.1 downscaled precipitation was a better input for the regional hydrological impact studies. However, downscaled precipitation from multiple GCMs is suggested for comprehensive impact studies.