Inner Mongolia is an important energy producer and the sixth-largest grain-supplying region in China. To address crucial water security challenges, the spatiotemporal variations in terrestrial water storage (TWS) and groundwater storage (GWS) in semiarid Inner Mongolia from April 2002 to January 2025 were evaluated on the basis of the synergistic use of multisource data, including satellite gravimetry, hydrological models, and meteorological data. There was a loss of TWS in Inner Mongolia (−1.69 ± 0.17 mm/year), which was caused mainly by the depletion of groundwater (−4.90 ± 0.12 mm/year), and it offset a slight increase in surface water (+3.21 ± 0.19 mm/year). Marked declines were clustered mainly in the central/southern regions (e.g., Ordos: GWS of −10.20 ± 0.19 mm/year), whereas the northeastern region (e.g., Hulun Buir) experienced an increase (+5.09 mm/year), which was related to abundant rainfall. Notably, the declining trend of GWS across all of Inner Mongolia before 2022 (−5.49 ± 0.17 mm/year) achieved an unprecedented reversal after 2022 (+17.80 ± 0.21 mm/year), indicating the significant influence of policy interventions and precipitation changes. In the central/eastern agro-pastoral zones, water loss was driven mainly by human-related activities such as coal mining and farming; in contrast, aridity in the west was worsened by climate variability. Therefore, it is crucial to formulate urgent water redistribution strategies, promote efficient irrigation methods, and improve monitoring systems for the purpose of protecting energy and food security and strengthening ecological adaptability in the context of climate change.