Evaporation from natural lakes and artificial reservoirs represents loss of water resources; unfortunately, existing estimations are based on simplified methods. Evaporation is a phenomenon related not only to in-lake thermodynamics but also to water surface area change driven by riverine in- and outflows. Thus, this study aims to reestimate evaporation on a global scale with a coupled model framework of hydro- and thermodynamics in rivers and lakes, of which estimate is consistent with previous ones. It was found that evaporation per area from reservoirs is more significant than that from natural lakes due to the difference in spatial distribution, and reservoir construction increases evaporative loss due to the warming up of water surface, in addition to an increase in surface area. The estimation of storage in each water body also showed that most of the residence time is caused by lakes. These results suggest that it is crucial to consider the thermodynamics of lakes and their interactions with rivers to estimate water resources and their quality.