Water conflicts between humans and ecosystems are key issues for sustainable water resource management. In the past decades, human-oriented regulation of water resources and construction of many hydraulic projects for hydropower generation, agricultural irrigation, and flood control has significantly altered natural flows in many rivers, resulting in increasing variances in water availabilities and flow regimes. For example, every year, a large amount of water is being diverted for agricultural irrigation in major river basins worldwide. Annually, over 70 % of water is extracted from the rivers to meet agricultural water needs in many countries. Particularly, a number of rivers are subjected to extremely high water extraction rates and the water can hardly reach the sea. Incessant declination in water availabilities has caused a series of impacts on many valuable aquatic habitats, such as riparian floodplains, wetlands, and estuaries. Due to population growth and economic development, enhanced amounts of freshwater are expected to be extracted to support human activities, further worsening such situations. Conflicts over water resources are thus intensive for human beings and ecosystems across the world. Many concerns are rising, particularly in many developing countries. For example, in China, since the early 1970s, the frequency of drying or ephemeral stream flows has been increasing in the Yellow River, which is the sixth largest river in the world. Since the early 1990s, drying took place annually in this river. Averagely, the time length without water in the lower reach of the river was approximately 100 days every year. Such extreme alterations have caused a cascade of adverse impacts on hydrological diversity, species distribution, and indigenous ecosystems in the Yellow River basin. This may eventually lead to unrecoverable effects on biodiversities, services, and even core functions of the associated ecosystems. Similarly, the other major river of China, i.e., the Yangtze River, is also subject to great alterations due to the construction of many mega water-related projects, such as the Three Gorges Dam and the South–North Water Transfer Project. Considering the pressure of stimulating economic growth in many developing countries across the world, similar constructions and projects have been undertaken. However, due to complexities of the associated river systems, as well as the interactions between humans and ecosystems, no clear results could be obtained regarding what unrecoverable and/or recoverable effects would happen because of such profound alterations. Moreover, the alterations may be multiplied by climate change, further affecting water availability and thus intensifying water competition between humans and ecosystems. In order to achieve sustainable water resource management, fostering a socio-economically and ecologically healthy consensus over water demands by humans and ecosystems is of great importance. Environmental flow that can be used to quantify the amount of water needed by a given ecosystem has become a competitive component with human water demand in watershed management. Thus, the management of water conflicts between humans and ecosystems in river basins is desired.