Water is the foundation of an arid ecological system, as the quantity and quality of surface water and groundwater determine its structure and function. The study on the relationship between water and ecosystem is the basis of ecosystem protection. Taking the Ejina delta, an extremely arid area located downstream of the Heihe River in northwestern China, as an example, this article gives an overviewe of the study in three aspects： （1） the groundwater table and salinity dynamics and their driving factors, （2） the groundwater depth and salt threshold of natural vegetation ecosystem, and （3） the impact evaluation of ecological flow control on Ejina natural vegetation. The authors point out the importance of the research into the relation between water and ecosystem and its key difficulties and weakness, and put forward strategies for promoting the study processes.