Water-lubricated rubber bearings are widely used in the propulsion shafting of military craft and ships. These bearings may wear down after a period of service, and consequently, their lubrication characteristics will change, affecting the operation of the shaft. Hydrodynamic lubrication characteristics of water-lubricated rubber bearings with partial wear at the bottom are studied by finite difference method. The steady-state characteristics of water-lubricated rubber bearings with wear and elastic deformation of rubber liner considered are solved with successive over-relaxation iteration method, and the dynamic characteristics are further calculated with finite perturbation method. The results show that water film thickness and distribution of water film pressure is significantly changed by wear. With the same eccentricity ratio, the maximum water film pressure, load capacity, attitude angle, and friction force are reduced by wear, but the friction coefficient is increased by wear. Under the same load, the minimum water film thickness and the maximum water film pressure are slightly affected by wear, the eccentricity ratio increases with the increase of wear, and the attitude angle and the friction coefficient decrease with the increase of wear. For large eccentricity ratios, the direct stiffness coefficients and direct damping coefficients are decreased by wear. The maximum allowable wear depth is approximately 1/6 of the bearing clearance.