Bosten Lake is a mid-latitude lake with water mainly supplied by melting ice and snow in the Tianshan Mountains. The depositional environment of the lake is spatially not uniform due to the proximity of the major inlet and the single outlet in the western part of the lake. The analytical results show that the carbon and oxygen isotopic composition of recent lake sediments is related to this specific lacustrine depositional environment and to the resulting carbonate mineralogy. In the southwestern lake region between the Kaidu River inlet and the Kongqi River outlet, carbon isotope composition (δ13C) values of the carbonate sediment (?1‰ to ?2‰) have no relation to the oxygen isotope composition of the carbonate (δ18O) values (?7‰ to ?8‰), with both isotopes showing a low variability. The carbonate content is low (<20%). Carbonate minerals analyzed by X-ray diffraction are mainly composed of calcite, while aragonite was not recorded. The salinity of the lake water is low in the estuary region as a result of the Kaidu River inflow. In comparison, the carbon and oxygen isotope values are higher in the middle and eastern parts of the lake, with δ13C values between approximately +0.5‰ and +3‰, and δ18O values between ?1‰ and ?5‰. There is a moderate correlation between the stable oxygen and carbon isotopes, with a coefficient of correlation r of approximately 0.63. This implies that the lake water has a relatively short residence time. Carbonate minerals constitute calcite and aragonite in the middle and eastern region of the lake. Aragonite and Mg–calcite are formed at higher lake water salinity and temperatures, and larger evaporation effects. More saline lake water in the middle and eastern region of the lake and the enhanced isotopic equilibrium between water and atmospheric CO2 cause the correlating carbon and oxygen isotope values determined for aragonite and Mg–calcite. Evaporation and biological processes are the main reasons for the salinity and carbonate mineralogy influence of the surface-sediment carbonate in Bosten Lake. The lake water residence time and the CO2 exchange between the atmosphere and the water body control the carbon and oxygen isotope composition of the carbonate sediment. In addition, organic matter pollution and decomposition result in the abnormally low carbon isotope values of the lake surface-sediment carbonate.