The impacts of environmental flow controls on the water table and chemistry of groundwater in the Ejina Delta, an arid inland river basin in northwest China, were investigated with field observations in 2001 and 2009. The results indicate that the shallow groundwater level rose by 0-2 m in the upper reaches of the east tributary of the Heihe River and in the areas of Saihantaolai-Dalaikubu during the period of environmental flow controls. The chemical constituents of the groundwater show a distinct spatial heterogeneity with the total dissolved solids (TDS) in the groundwater increasing from the periphery towards the depocenter of the Ejina Basin. In addition, the rate of groundwater cycling in the south of the Ejina Delta increased, and the mineralization of groundwater declined, while the overall mineralization and salinity increased in the northern regions, especially in the depocenter of the Ejina Basin. Since shallow groundwater is important to the ecology of arid regions, and because understanding the changes in the shallow groundwater environment (groundwater level and hydrochemistry) in response to environmental flow controls is essential for the sustainable improvement of the ecological environment, the results of this paper can be used as a reference for watershed water resources planning and management to help maintain the health and proper function of rivers in arid regions.