Highlights What are the main findings? Multi-mission satellite altimetry revealed extreme water level rises up to 5.12 m (21.47 Gt) in Lake Zaysan during 2010, 2013, and 2024. Strong correlation (r = 0.95) between discharge anomalies and lake levels confirms intense snowmelt runoff as the primary driver of extreme events. What are the implications of the main findings? Extreme events are driven by negative Arctic Oscillation phases (2010, 2013) and strong El Ni & ntilde;o events (2016, 2024). The monitoring approach provides baseline data for transboundary water management in climate-sensitive Central Asian basins.Highlights What are the main findings? Multi-mission satellite altimetry revealed extreme water level rises up to 5.12 m (21.47 Gt) in Lake Zaysan during 2010, 2013, and 2024. Strong correlation (r = 0.95) between discharge anomalies and lake levels confirms intense snowmelt runoff as the primary driver of extreme events. What are the implications of the main findings? Extreme events are driven by negative Arctic Oscillation phases (2010, 2013) and strong El Ni & ntilde;o events (2016, 2024). The monitoring approach provides baseline data for transboundary water management in climate-sensitive Central Asian basins.Abstract 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.