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We present a case study of physical and chemical indicators and isotope characteristics of Lake Nuoertu, one of the largest and deepest lakes of the Badain Jaran Desert. We analyze the concentrations of eight ions, total dissolved solids, and stable isotope composition of the lake and groundwater, as well as radioactive isotope tritium concentration in groundwater. The results show that annual and seasonal variations of the physical and chemical characteristics of Lake Nuoertu water are significantly greater than those of groundwater. The lake is uniformly mixed in the horizontal and vertical directions, and the hydrochemical types of the lake at different depths are consistent for Na-Cl-CO3-(SO4). Stable isotope composition of the lake and groundwater at Nuoertu is distributed along the local evaporation line (EL) slope, which is less than the slope of the global meteoric water line. The comparatively small slope shows the characteristic strong evaporation in the study area. Lake water isotopes are mostly in the upper right corner of the EL, whereas groundwater is mostly in the lower left corner. The main recharge source of Nuoertu lake water is groundwater, in combination with lake water and groundwater level change. The age of tufa springs around Nuoertu is about 75-80 a, which shows that the initial recharge source of the lake is a mix between modern and 1952 or older; however, further research is required.