Marine water-lubricated polymer bearings support the propeller shaft that stretches out of the ship. The bending deformation of propeller shaft often leads to journal misalignment, significantly impacting the bearing performance. In this paper, a mixed lubrication model for water-lubricated polymer bearing is established considering the effect of journal misalignment, liner elastic deformation, and local turbulence. The influence of key structural and operating parameters on the performance of water-lubricated bearing with journal misalignment is investigated. The results show that the journal misalignment significantly reduces the load-carrying capacity, deteriorates the bearing tribological characteristics, and may cause different axial sections of the bearing to be in different lubrication regimes. Compared with aligned bearings, increasing the length–diameter ratio to improve the load-carrying capacity is significantly weakened for misaligned bearings. Increasing the liner thickness and the load improves axial uniformity of pressure distribution of misaligned bearings. A relatively large clearance ratio decreases the load-carrying capacity and increases the friction coefficient of bearings in the mixed lubrication regime.