Jinan, China, is famous for its springs. However, societal and economic development over the past decades has detrimentally altered the natural water cycle in the spring area. Managed aquifer recharge (MAR) is an effective measure to ensure the normal gushing of springs. Balancing water resource utilisation, ecological effects, and water quality risks is not always easy to implement. This study focused on the potential effects of MAR projects that divert water from multiple local surface water sites, e.g., the Yellow River and South-to-North Water Diversion (SNWD) Project. A numerical simulation model for the entire spring area was built using MODFLOW and MT3DMS. The SNWD Project diverts water with relatively high total dissolved solids (TDS) to the Yufu River, which consequently recharges groundwater and poses a potential risk to the downstream karst water in the Jinan Spring area. Different simulation scenarios were set, and the results showed that the 90% recovery ratio scheme yields the highest TDS reduction efficiency as well as the largest karst water extraction volume. In addition, the water table remains stable as a whole. The benefits of the designed scheme are multifold, including improving water quality up to Standard III groundwater quality and meeting the water needs of the economy. The study provides a novel method of addressing the groundwater quality risks posed by artificial recharge.