In this paper, the effects of manufacturing error and micro-groove on the static, dynamic and stability characteristics of water-lubricated journal bearings (WLJBs) are investigated. Mathematical expressions of manufacturing errors and surface micro-groove are presented, and the Reynolds equations with steady and unsteady states are calculated by using the linear perturbative method and the finite difference technology. According to the developed model, the effects of the waviness magnitude, spatial number, and phase angle for circumferential errors, as well as the concavity, convexity, and taper for axial errors on the film thickness distribution, fluid pressure distribution, bearing capacity, coefficient of friction, side leakage flow rate, attitude angle, stiffness coefficient, damping coefficient, threshold speed and whirl frequency ratio of WLJBs are evaluated. Simulation results demonstrate that fluid film thickness distribution and fluid pressure distribution are significantly affected by manufacturing errors and micro-groove. Compared with axial manufacturing errors, circumferential manufacturing errors cause an inhomogeneous distribution of fluid pressure and morphological transformation in the high-pressure zone. The variation rules for the lubrication performance of bearings with circumferential waviness, concavity, convexity, and taper errors are not consistent at various eccentricity ratios. The magnitude of the concavity and taper errors may have an improving effect on the bearing performance, whereas circumferential waviness and convexity error play a negative role. Moreover, the micro-groove with partial distribution enhances the hydrodynamic effect in the bearing clearance. Numerical simulations can provide a valuable reference for the manufacturing and design of bearing systems.