Drought frequently occurs in North China and is the most damaging disaster in this region owing to its large-scale impact on hydrology and ecosystems. This is the main reason that China implemented the world-famous South-to-North Water Diversion (SNWD) project. However, quantifying the drought-induced water deficit at a regional scale is still a significant challenge. Gravity Recovery and Climate Experiment (GRACE) satellites monitor temporal variations in the Earth’s gravitational potential and provide quality data sets for water storage analysis. In this study, we quantify the water deficit over North China in the context of the implementation of the SNWD project by focusing on a recent drought event, the 2009/10 drought, and identifying its onset, persistence, and recovery. As confirmed with ground-measured and land surface modelling data sets, GRACE can successfully capture temporal variations in total water storage. Total water storage shows a declining trend, reaching a low point during the 2009/10 drought with a water storage deficit of up to 25 km<sup>3</sup> (~ 22 mm). Groundwater storage shows a similar pattern, with a trend of −6.97 mm yr<sup>−1</sup>. Together with the water deficit, vegetation growth is substantially restricted, as indicated by a reduction in the leaf area index. The amount of water transfer by the SNWD project can roughly meet the water deficit in North China but the effectiveness of the SNWD will depends on specific water configuration strategies.