The level of groundwater has fallen dramatically in the plain, and several obvious cones of depression in the groundwater surface around waterworks have expanded, because of groundwater over-drafting in Beijing. This condition has led to reductions in available groundwater resources, and has even restricted the economic development of Beijing. However, an opportunity has been provided for groundwater recharge, since considerable storage space has been created by this overexploitation. At the beginning of the South-to-North Water Diversion, more water will be transferred to Beijing, because of the supporting infrastructure that is under construction in other cities. Therefore, the underground reservoir in Miyun, Huairou and Shunyi (MHS) district was taken as the study object, and geological exploration and GIS overlay techniques were used to determine the extent and storage capacity of this underground reservoir. The rivers in MHS district were investigated to identify which ones provide suitable places for recharge. Furthermore, a numerical model was built to forecast the groundwater flow field and water level, and an optimal storage program was proposed. The results of this study provide technical guidance for recharge, as well as the safe storage and rational use of the water provided by the South-to-North Water Diversion.