<p>In foundation pit design for metro systems, waterproof diaphragm walls play a crucial role in controlling groundwater and stabilizing soil. Particularly in areas with thick aquifers, extending the diaphragm wall is essential to prevent groundwater from flowing into the foundation pit. In this study, a series of experiments and numerical simulations were utilized to study groundwater seepage and deformation of suspended waterproof structures, with the goal of optimizing material usage. We explored the deformation mechanisms induced by seepage during foundation pit dewatering, and investigated the relationship between groundwater drawdown and deformation of the structure. Our findings indicate that increasing the burial depth of the waterproof structure decreases the duration of water pumping and reduces the volume of water extracted, thereby enhancing the efficiency of dewatering. The maximum horizontal displacement of the waterproof structure is found to be influenced by both the groundwater drawdown and the insertion ratio of the structure. However, the location of this maximum displacement only depends on the groundwater drawdown. Additionally, the bottom displacement and its location within the waterproof structure are both governed by the groundwater drawdown and the structure’s insertion ratio. This research provides insights into deformation mechanisms and may serve as a reference for future design of underground waterproof structures in aquifer geological conditions.</p>