The combination of recharge project and precipitation project is an effective measure that takes into account the safety of the project and the protection of groundwater resources. The central urban area is restricted by the layout of recharge sites and water pipelines. The recharge area is close to the precipitation area, and the scope of recharge and precipitation affect overlap. At this time, recharge and precipitation will inevitably have mutual effects. Taking the precipitation recharge project of a wind well sand and pebble diving layer in a subway project in Beijing as an example, combined with field tests, theoretical derivation, and numerical analysis, it is concluded that the recharge near the same layer will increase the flooding of the foundation pit by about 40%. The research has certain engineering guiding significance for the recharge project of sandy pebbles and other highly permeable submerged aquifers.