The overexploitation of groundwater (GW) and the associated environmental consequences are a cause for concern worldwide. Despite widespread unease about replenishing GW through, for example, water diversion schemes, there have been few comprehensive impact assessments, particularly for large urban areas that are undergoing rapid development to achieve regional goals. Using gravity recovery and climate experiment (GRACE) satellite data, we quantified the changes in GW storage from 2002 to 2017 and the reasons for the changes across a large-scale urban agglomeration in China (Beijing-Tianjin-Hebei, BTH) with a serious GW deficit. We found that, at the aggregate scale, from 2002 to 2017, the GW storage over the entire BTH declined at an average annual rate of 1.20 cm, but the rate of decline decreased markedly after 2010. At the city scale, the rates of decline in the GW storage between different cities varied but were strongly spatially correlated. The spatial correlation pattern was inverted from north to south and corresponded with the unbalanced diversion of water between cities from the South-to-North Water Transfer Project and was also affected by the policy of transferring industrial water from Beijing to the central and southern plains of BTH. Human-related factors were the most significant drivers of the changes in GW storage and, of these, agricultural water consumption had the most effect on the changes in GW storage. To protect GW supplies in large-scale urban agglomerations, regionally diverted water allocations should be coordinated with other development strategies, such as the regional industry distribution and transfer policy and agricultural water use management.