This paper highlighted the importance of research on green water in watershed and proposed key scientific issues for future studies: (1) Estimation or measurement of green water flow and scaling: Green water are considered to comprise both evaporation and transpiration components. The evaporation component is made up of evaporation of intercepted water evaporation from plant surfaces as well as free water surfaces and evaporation from the soil. There are challenges associated with estimating green water flow. First, difficulties exist in determining the spatial and temporal variation of evaporation over large areas. Secondly there are very few methods which allow for estimates of transpiration and evaporation separately. The promising methods for estimates of green water flow may be the application of the scintillation method and remote sensing combination. (2) Formation, transformation and ecohydrological impacts of green water flow in the watershed: Formation of green water is very complicated the in the upper, middle and lower reaches of the watershed due to human activities (land use/cover changes) and climate impacts; in the upper reach of the inland basin of China, green water is mainly transformed into blue water, but in the middle and lower reaches, blue water is mainly transformed into green water, both of them are interlinked in the hydrological cycle on the watershed scale. Researches should also pay attention to unsaturated zone and soil structure quantification for dynamic green water flow in the soil profile, and the spatial scale should include microscopic (e.g., pores aggregates), mesoscopic (e.g., pedons and catenas), and macroscopic (e.g., watersheds, regional, and global) scales. (3) Assessment and management of green water flow: Assessment of green water includes total amount of green water and available green water, which still needs further study. In a word, we need to consider rainfall as the basic water resources and to incorporate green water and blue into integrity to harmonize water consumption for ecological, domestic and productive uses in the upper, middle and lower reaches of the watershed, thus fully exploiting nonproductive green water and balance water between nature and human.