In this study, we explore how the differences in soil moisture accounting affect the estimation of actual soil evaporation (E) and transpiration (T). The main objective is, therefore, a comparative assessment of a vapor flux estimation method which has explicit soil moisture accounting, against a vapor flux estimation method that uses satellite observed soil moisture data. Three methods with different representations of water supply dynamics are compared: (1) ETLook, wherein E and T are estimated using Advanced Microwave Scanning Radiometer – Earth Observing System (AMSR-E) derived soil moisture data; (2) a simple evaporation transpiration scheme (SETS) that has a similar vaporization representation as ETLook but with soil moisture accounting based on the MOSAIC Land Surface Model; and (3) SETS-AMS which is similar to SETS except that the AMSR-E derived soil moisture controls the top layer mass balance. The schemes are compared on the Indus River Basin for the year 2007 at 1 km spatial resolution. The results suggest that downward soil water flux influences the estimation of E and T. This effect is especially dominant in areas with high soil moisture content. The comparative assessment reveals how lack of explicit soil moisture accounting may lead to an overestimation of E and underestimation of T, especially in irrigated areas.