summary The Lower Tarim River in NW China is under severe ecosystem degradation due to stopped stream flow and diminished groundwater recharge. Since year 2000, eight water diversions from the upper stream and from the neighboring Kaidu–Kongque River have been implemented to alleviate the ecosystem disaster. In order to assess the effectiveness of the water diversion project and to identify proper tracers of groundwater dynamics, we sampled the riparian groundwater system in 2007 and 2008 along the 350 km-long river channel through the 40 monitoring wells situated along nine transects perpendicular to the river and three soil profiles. Measurements on the samples have included environmental isotopes ( 18 O, 2 H, 3 H) and water chemistry. The results show that remarkable changes have been induced by the water diversions. The observed response of riparian groundwater system includes general decrease in total dissolved solid (TDS) and rise of water table. Scope with greater than 1 m rise in water table is within �700 m from the riverbank in the upper segments and �300 m in the lower ones. Greater rise of water table occurs near the river bank. Tritium data show that the extent of modern recharge (since 1960s), including that from the diverted water, is limited to 600 m from the riverbank at the upper segments and 200 m at the lower ones. Stable isotopes show that groundwaters, regardless of modern or pre-modern, are enriched in heavy isotopes and are plotted in parallel to the meteoric water line in the d–d plot, attributed to evaporation during recharge. Groundwater is generally of Na–Mg–Cl–SO4 type and is formed by dissolution of minerals, such as halite, sulfate, and carbonates, based on component correlation matrices analysis. The salinity of groundwater is mainly affected by that of the diverted water and of the local antecedent groundwater, salts in the unsaturated zone, evapotranspiration during recharge. As the zone of smaller groundwater depth (less than 5 m) suitable for the most existing Populus euphratica and Tamarix ramosissima, the main species targeted by the rescue effort, restricts to 200 m from the riverbank, and narrows down towards downstream, long-term stability of the ecosystem cannot be achieved by the current water diversion scheme and regulating/saving water in source-streams and the Upper/Middle Tarim River is crucial for continuing water diversion.