Water inrush damage was observed in a shield tunnel under the Yangtze River. This is a rare occurrence in shield tunnels, necessitating determination of its causes and establishment of corresponding targeted recovery measures. In the current study we investigated the hydrogeological and geotechnical conditions of the area, evaluated possible contributors to the damage and determined a biogas leakage as the cause. Based on theoretical analysis, we proposed a freezing recovery programme 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 ring 950. Numerical simulations prior to the actual construction were performed to analyse the frozen range and frozen effect. Results revealed the temperature in the frozen area to be below –1°C, meeting construction requirements. The proposed freezing technology was verified using the monitoring data from the thermometer hole. This work provides a way to the recovery of shield tunnels in deep-water areas.