Groundwater treatment in ecological replenishment areas is a prerequisite for the continuation of submerged underground projects, while groundwater treatment and project continuation inevitably impact the surrounding environment, leading to issues such as existing structure settlement. To address this, the study focuses on the continuation of the transfer hall project at Jingfengmen Station on Beijing Metro Line 19, employing a combination of stress-seepage coupling numerical simulation and field measurements to compare the water control effects and deformation impacts on adjacent shield tunnels between two groundwater treatment measures: dewatering-pressure relief combined with grouting for water stoppage versus pure dewatering. The findings reveal that the combined measure of dewatering-pressure relief plus grouting for water stoppage effectively controls groundwater seepage and significantly reduces the risk of pit surging. The rising groundwater level and treatment, along with the continuation of the submerged project, cause adjacent shield tunnel segments to exhibit multiple stages of deformation and settlement, including lateral bias toward the pit side, overall uplift, and subsequent deformation and subsidence toward the pit side. The repeated transitions in segment deformation lead to irreversible deformation at joints, stress concentration, increased misalignment and opening at joints. Compared to pure dewatering measures, the combined approach reduces segment deformation, misalignment, and surface settlement by 23.7% to 65.32%, demonstrating superior protection for existing shield tunnels and surrounding strata, making it more suitable for groundwater treatment in environmentally sensitive areas. The research outcomes provide valuable insights for underground construction in ecological replenishment influence zones.