Water inrush damage was observed in a shield tunnel under the Yangtze River. This is a rare occurrence in shield tunnels and thus requires the determination its causes and the establishment of the corresponding targeted recovery measures. In the current study we investigated the hydrogeological and geotechnical conditions of the area and evaluated the possible contributors to the damage mechanism, determining a biogas leakage as the cause. Based on the theoretical analysis, we proposed a freezing recovery program with the following measures: (i) dewater the piezometric head and release the biogas in the soils; (ii) create a freezing curtain; and (iii) drain the accumulated water and build a permanent occlusion at the 950th ring. Numerical simulations prior to the actual construction were performed to analyze the frozen range and frozen effect. Results revealed the temperature in the frozen area to be below -1°C, meeting the construction requirements. The proposed freezing technology was verified using the monitoring data of the thermometer hole. This work provides a way to the recovery of shield tunnels in deep-water areas.