A manipulator/vehicle system floating on water consists of a vehicle with a manipulator attached to it. Similar to the space manipulator system, the system on water is not fixed to an inertial coordinate system. So, external forces affect the motion of the system. In this paper, we propose an algorithm for controlling the position and orientation of the end-effector of the manipulator/vehicle system in an inertial coordinate system under the assumption that the stability of the vehicle is maintained. We derive the kinematics of the system and propose a trajectory tracking control algorithm based on the resolved motion rate control, then prove convergence of the control algorithm using the Lyapunov’s method. Experimental results illustrate the validity of the proposed control algorithm.