A case is presented about damages due to leakage and inrushing water that developed in the segmented pre-casted concrete liner of a shield tunnel under the Yangtze River. Various possible causes were considered to explain the damage mechanism. The opening and distribution due to differential settlement caused by the leakage of biogas or water in the shield tunnel were analyzed. The damage mechanism of the aquifuge, which occurred under the tunnel through exertion of a high piezometric head in the lower confined aquifer, was analyzed. The tensile-shear damage mechanism of the aquifuge was studied, and the judgment formulas, which were used to determine whether surface water bursting occurred, were derived. Two dewatering recovery programs were simulated by the finite difference method in conjunction with MODFLOW software. From the simulation results, the hydraulic gradient and settlements caused by decreased pore pressure were calculated. The optimal dewatering scheme and protection measurements are suggested.