Abstract: This study focuses on the issue of water leakage in the retaining structures of foundation pits in sandy composite strata and the corresponding control measures. Based on the excavation of the foundation pit for the Yanghu Block Post on Guangzhou-Huadu Intercity Railway, numerical simulations and field testing were conducted to analyze the effects of water leakage on soil, structural deformation, and flow field distribution. The effectiveness of three treatment measures against water leakage—back-filling soil, grouting reinforcement outside the pit, and dewatering outside the pit—was compared. The results indicate: (1) When the structure experiences slight water seepage, the horizontal displacement and deformation of the soil and structure is significant, while the vertical displacement is relatively small. (2) Near the water seepage point, sand particles in the soil are lost, reducing strength and increasing horizontal deformation. The water seepage area of the diaphragm wall experiences significant water-soil pressure, resulting in a "bulging" curvature, with the maximum horizontal displacement increasing to 15.13 mm. The pore water pressure at the defect area significantly increases, which exacerbates the wall deformation. (3) The three treatment measures can effectively control both water seepage and structural deformation. The dewatering treatment outside the pit shows the best effect in controlling structural deformation, while grouting reinforcement outside the pit is more effective in controlling deformation in the depth direction. (4) The above treatment measures have shown good control effects on-site, significantly reducing the wall deformation rate and gradually restoring it.