A system for lifting thrusters of floating vessels enabling for maintenance to be safely provided on the thrusters, the system comprising: a. a lifting means with a flexible lift line and a connector for extending into a thruster well formed from a thruster well wall and a thruster well bottom flange of a floating vessel to engage a lifting eye of a thruster or to engage a portion of the thruster; b. a moveable transport device connected to the lifting means for transporting the thruster or the portion of the thruster; c. a plurality of clamps for securing a thruster mounting flange to the thruster well bottom flange, wherein each clamp comprises: an actuator adapted to extend and retract and a linkage connected to the actuator for engagement with one of a plurality of clevis plates, and wherein each clevis plate is secured to an inside surface of the thruster well wall; d. a conduit for controllably allowing water to flow into the thruster well; e. a controller for opening and closing the conduit to allow the water to flow into or out of the thruster well; f. a pump for pumping the water out of the thruster well; g. at least one seal adjacent the thruster mounting flange for providing a water tight connection between the thruster well bottom flange and the thruster mounting flange; h. a plurality of alignment guide plates disposed concentrically around the thruster in the thruster well and extending from proximate the thruster well bottom flange to a thruster well wall top of the thruster well wall for a rough alignment of the thruster to the thruster mounting flange; and i. a plurality of fasteners for securing the thruster mounting flange to the thruster well bottom flange. a. a lifting means with a flexible lift line and a connector for extending into a thruster well formed from a thruster well wall and a thruster well bottom flange of a floating vessel to engage a lifting eye of a thruster or to engage a portion of the thruster; b. a moveable transport device connected to the lifting means for transporting the thruster or the portion of the thruster; c. a plurality of clamps for securing a thruster mounting flange to the thruster well bottom flange, wherein each clamp comprises: an actuator adapted to extend and retract and a linkage connected to the actuator for engagement with one of a plurality of clevis plates, and wherein each clevis plate is secured to an inside surface of the thruster well wall; d. a conduit for controllably allowing water to flow into the thruster well; e. a controller for opening and closing the conduit to allow the water to flow into or out of the thruster well; f. a pump for pumping the water out of the thruster well; g. at least one seal adjacent the thruster mounting flange for providing a water tight connection between the thruster well bottom flange and the thruster mounting flange; h. a plurality of alignment guide plates disposed concentrically around the thruster in the thruster well and extending from proximate the thruster well bottom flange to a thruster well wall top of the thruster well wall for a rough alignment of the thruster to the thruster mounting flange; and i. a plurality of fasteners for securing the thruster mounting flange to the thruster well bottom flange.