Water ecosystem service flow is currently a hot topic in the field of ecosystem services. Assessing the ecosystem service flow from a dynamic perspective can help better analyze the contradictions between supply and demand of water ecosystem services, so as to achieve scientific management and allocation of water resources to improve human well-being. This paper summarizes the existing literature on water ecosystem service flows, describes definition and classification, the scale characteristics and carrier characteristics of the water ecosystem service flows, and analyses domestic and international distribution of research regions and study objects. The concept of water ecosystem service flow has been described mainly from two perspectives. One focuses on the path of the water ecosystem service flow and the other focuses on the outcome of the water ecosystem service flow. Different research perspectives have made the concepts of water ecosystem service flow not yet unified. There are also differences in the main influencing factors of water ecosystem service flows at different spatial and temporal scales. Meanwhile, water as the main carrier of water ecosystem service flows, has brought great convenience to the research with its figurative biophysical properties. Then the basic processes and methods of current water ecosystem service flow assessment are sorted out, mainly including data collection, water ecosystem service supply and demand calculation, assessment of material flow of water ecosystem services and assessment of value flow of water ecosystem services. Current applications of water ecosystem service flows to water resources management are summarized, including the assessment of regional water ecosystem security, watershed ecological compensation, and flood management. The shortcomings of current researches on water ecosystem service flows are discussed as follows: (1) fewer available models for analyzing water ecosystem service flow and more defects in the existing network models; (2) a lack of trade-offs and synergistic analyses of water ecosystem service flows and other service flows; (3) insufficient research on the interactions between water ecosystem services and natural ecosystems. Finally, the future prospects for research on water ecosystem service flows are proposed to: (1) develop more adaptable models for water ecosystem service flows; (2) integrate research at multiple scales; and (3) perform coupled analyses of water ecosystem service flows, with a view to promoting the research on water ecosystem service flows in a more systematic as well as scientific direction.