In order to study the influence of water-lubricated bearings on the vibration of the marine magnetic pump, the vibration characteristics of the marine magnetic pump under different flow rates and bearing structural parameters (bearing clearance, eccentricity, and length–diameter ratio) were numerically analyzed. The internal flow fields of marine magnetic pumps and water-lubricated bearing were numerically calculated, and experimental verification of their external characteristics results was conducted. The results show that the vibration velocity level of the pump increases with the increase in the bearing clearance and the bearing eccentricity, and the vibration velocity level of the pump gradually decreases with the increase in the bearing length–diameter ratio. The clearance has the greatest influence on the vibration of the pump, the length–diameter ratio the second, and the eccentricity the smallest. The peak value of vibration velocity at the pump outlet at the vibration measurement point is the highest, the peak value of vibration velocity at the pump inlet is second, and the peak value of vibration velocity at the pump foot is the smallest. However, the peak value of vibration velocity at the pump inlet is most sensitive to changes in operating conditions and bearing structural parameters, with a maximum increase of 6.2 dB. Therefore, the change in the peak value of vibration velocity at the pump inlet can be used as the main indicator for monitoring the operating status of bearings.