The evolutionary stages of the different lakes in the Badain Jaran Desert (BJD) are unknown, and there is a need to elucidate the hydrological implications of the hydrodynamic environmental differences among these lakes. In this study, a stable isotope mass balance model incorporating the effect of evaporation from the lake basins was developed, and the model was used to calculate the remaining water fraction f of 94 lakes relative to the high lake levels in the Middle Holocene, as well as the groundwater recharge rate ${\mathrm{\chi }}_{\mathrm{G}}$ to the lakes. The results show that only 10–20 % (average of 15 %) of the original lake water remains. One-third of the lakes have become terminal lakes, and half are still gradually drying. If the climatic conditions remain unchanged, the water levels of these lakes will drop by an average of 11 mm per year. ${\mathrm{\chi }}_{\mathrm{G}}$ has a certain degree of correlation with elevation, suggesting the likely presence of more water recharge sources for the north lakes, which may include the Beida Mountains and the Zongnai Mountains. The total annual groundwater recharge to all of the lakes in the BJD is 1.63 × 10⁷ m³/yr. The δ¹⁸O evolution model of a typical lake (Cherigele Lake) reveals that humidity h and atmospheric vapor δ_a¹⁸O play the leading role in the evolution of the lake δ¹⁸O, suggesting that this model may serve as a tool for estimating lake evaporation and for reconstructing the paleoclimate. The findings of this study provide support for analyzing the evolution and future trends of lakes in arid desert areas, as well as deeper insights into the water cycle in the BJD.