Fatigue of prestressing wires during service can lead to a loss of prestressing force, which directly affects the load-bearing and deformation characteristics of the water conveyance tunnel structure. A finite element model of the double-layer lining structure of the water conveyance tunnel was established to investigate the mechanical response of the tunnel components under different prestress loss conditions. The results show that: With the increasing of prestress loss, the peak stress of bolts continues to rise but remains below the yield strength design value; the stress distribution of internal reinforcement is relatively uniform; the tensile trend of segmental reinforcement and segmental concrete weakens with increasing prestress loss during water flow; as prestress loss grows, the transverse elliptical deformation trend of internal concrete lining becomes more pronounced; analyzing the joint stress state of components reveals that under prestress loss conditions, the overall structure enters the joint stress state prematurely, with the greatest impact on bolts. These findings provide a reference for similar prestressed water conveyance tunnels.