In the first-level terrace of the Yangtze River in Wuhan which is featured with typical dual-structure strata where the confined groundwater is connected with the Yangtze River and the Hanjiang River, the fluctuation of groundwater level would jeopardize foundation pit excavation, particularly when there is leakage point on the diaphragm wall. Assume that water or sand penetration is induced by groundwater level rising, the expansion of leakage point would threaten the stability of diaphragm wall or even give rise to ground settlement outside the wall. With a foundation pit excavation in Hankou, Wuhan, as a case study, we investigated the deformation and stability of foundation pit in the presence of leakage caused by groundwater level rising via centrifugal model test. In the presence of a weak point, when confined groundwater level rose above the leakage point, water and sand gradually penetrated, which further led to more significant settlement of the ground surface outside of the wall in a large scope. Such deformation differs from that induced by excavation. The research finding offers reference for the design and construction of foundation pits in the first-level terrace of the Yangtze River in Wuhan.