Effective control of the health operating condition of multi-support, ultra-long shaft system water-lubricated stern bearings is crucial for supporting the intelligent maintenance and health management of ships. This study investigates the failure modes of water-lubricated stern bearings and focuses on the critical failure modes of abnormal wear and high-temperature meltdown to analyze the mechanisms and influencing factors of these failures. It discusses the conditions for healthy operation of water-lubricated stern bearings, as well as methods for controlling lubrication and temperature rise. Based on this, controllable parameters for the healthy operation of water-lubricated stern bearings were selected, an experimental rig was constructed, and experiments were conducted using SF-2A material water-lubricated bearings. The experimental results indicate that by controlling parameters such as shaft rotational speed, inlet lubrication water temperature, clear-water lubrication, sediment-laden-water lubrication, bearing specific pressure, and the surface morphology of the bearing liner, the velocity characteristics, lubrication characteristics, and temperature rise characteristics of the bearings can be effectively altered. The sensitivity of the lubrication and temperature rise characteristics of SF-2A material water-lubricated stern bearings to controllable parameters varies under different environmental conditions. The study finds that precise control of these parameters can improve the operating condition and reliability of water-lubricated bearings.