The Zoige Plateau, situated on the eastern edge of the Qinghai-Tibet Plateau, exhibits complex groundwater dynamics influenced by alpine hydrological processes and climatic variability. This study investigates the spatiotemporal evolution of groundwater in the Zoige alpine basin from 2002 to 2024 using an integrated approach that combines in-situ monitoring, GRACE satellite observations, and GLDAS model outputs. Using the Innovative Trend Analysis (ITA) method alongside conventional statistical techniques, we identified both seasonal fluctuations and long-term depletion trends. Groundwater levels exhibited clear wet–dry season contrasts and a cumulative decline of up to 2.3 m in grassland flatlands, corresponding to a long-term depletion rate of 0.4 cm/a as indicated by GRACE-derived groundwater storage. The most significant declines occurred in grassland zones, driven by wetland degradation and elevated evapotranspiration, while mountain regions showed slower losses (~0.1 cm/a) primarily supported by sustained snowmelt recharge. Through the integration of multi-source datasets, this study highlights the spatial heterogeneity and key drivers of groundwater variation, providing a robust framework for sustainable groundwater management under climatic and anthropogenic pressures in alpine wetland systems.