Lake water level variation, reflecting the dynamic balance between water input and loss, is a crucial indicator of climate change and regional hydrological cycles. This is particularly significant in arid Central Asia, where lakes are vital surface water resources and key to ecosystem stability. This study systematically reconstructed water level changes of Lake Zaysan and Lake Ulungur from 2003 to 2024 using high-precision altimetry data from ICESat, CryoSat-2, and ICESat-2 satellites. Results indicate that Lake Zaysan experienced significant water level fluctuations of 5.01 m (21.01 Gt water mass change, where 1 Gt = 10⁹ metric tons) in 2010, 5.12 m (21.47 Gt) in 2013, and 3.53 m (14.80 Gt) in 2024. Lake Ulungur also exhibited notable water level changes during the same period. Our study reveals that water level variations in both lakes are primarily controlled by runoff processes. A highly significant positive correlation exists between lake level anomalies and discharge anomalies. Conversely, the low correlation between water levels and precipitation indicates a pronounced lagged effect of snowfall, as lake water level fluctuations are driven by a combination of spring snowmelt runoff and summer precipitation. Furthermore, these findings highlight the sensitive response of these Central Asian lakes to environmental changes under climate warming. Our study enriches observational data on regional lake dynamics and provides a scientific basis for water resource management and future climate adaptation strategies in arid regions.