The Chad Basin is the main source of fresh water to over 30 million people in the semi-arid Sahel region, and long-term evaluation of groundwater resources is crucial for sustainable abstraction of fresh water, water security for the region, and humanitarian resilience. Using the GRACE/GRACE-FO satellite gravimetry and GLDAS land surface modelling, this study was used to assess the hydrological variations in one of the least data-rich and most water-drafted transboundary basins in the world. Results show an important hydrogeological paradox. The overall trend in the basin-scale water mass, as revealed by Total Water Storage Anomaly (TWSA), is a strong increase of +5.91 mm/year (R² = 0.70). However, recoverable water components are diminishing, with surface water, soil moisture, and Groundwater Storage Anomaly (GWSA) decreasing at −1.04, −1.02, and 0.02 mm/year, respectively. This means that a higher absolute amount of water stored does not necessarily lead to an increase in groundwater recharge, probably because of high evaporation, extraction pressures, and hydrogeological conditions. Spatial analysis also reveals areas of critical groundwater depletion along the western boundary of the basin, especially across the northeastern part of Nigeria, where groundwater extraction is high. Rainfall trends are weak (+1.65 mm/year) and not significantly correlated with groundwater storage (r = −0.176), indicating that recharge efficiency to the deep aquifers is poor. The overall conclusion is that the anthropogenic pressures on water scarcity are growing, and the use of evidence-based transboundary governance, regulation of groundwater abstraction, and targeted Managed Aquifer Recharge strategies is needed.