In this study, the revised Remote Sensing-Penman Monteith model (RS-PM) was used to scale up evapotranspiration (ET) over the entire Yukon River Basin (YRB) from three eddy covariance (EC) towers covering major vegetation types. We determined model parameters and uncertainty using a Bayesian-based method in the three EC sites. The 95 % confidence interval for the aggregate ecosystem ET ranged from 233 to 396 mm yr−1 with an average of 319 mm yr−1. The mean difference between precipitation and evapotranspiration (W) was 171 mm yr−1 with a 95 % confidence interval of 94–257 mm yr−1. The YRB region showed a slight increasing trend in annual precipitation for the 1982–2009 time period, while ET showed a significant increasing trend of 6.6 mm decade−1. As a whole, annual W showed a drying trend over YRB region.