Excavation in a rock mass leads to the perturbation of the stress regime, often creating a stress-relieved, locally weakened zone known as the disturbed zone. This paper presents the results of in situ studies that were carried out both in the central rock barrier (or separation block) between the shiplift and the temporary shiplock and in the northern slope of the permanent shiplock of the Three Gorges Project. The vertical extent of the disturbed zone was determined jointly by cross-hole seismic wave penetration testing and borehole elastic modulus testing, and the horizontal extent was assessed by monitoring and evaluating the deformation characteristics. Compared with the undisturbed rock mass, the P-wave velocity of the disturbed zone was reduced by 34–38% and the borehole elastic modulus by 12–31%. The reductions were caused by the opening of primary structural planes or the extension of apertures due to local sliding along the structural planes. In the disturbed zone, no newly formed fractured planes were found. The observed disturbed zone was compared with the tensile stress zones and the shear-damaged zones calculated by the finite element method. A rock reinforcement scheme was recommended and implemented.