In this paper, we present a comprehensive trajectory tracking framework for cooperative manipulation scenarios involving marine surface ships. Our experimental platform is a small boat equipped with six thrusters, but the technique presented here can be applied to a multiship manipulation scenario such as a group of autonomous tugboats transporting a disabled ship or unactuated barge. The primary challenges of this undertaking are as follows: (1) the actuators are unidirectional and experience saturation; (2) the hydrodynamics of the system are difficult to characterize; and (3) obtaining acceptable performance under field conditions (i.e., global positioning system errors, wind, waves, etc.) is arduous. To address these issues, we present a framework that includes trajectory generation, tracking control, and force allocation that, despite actuator limitations, results in asymptotically convergent trajectory tracking. In addition, the controller employs an adaptive feedback law to compensate for unknown-difficult to measure-hydrodynamic parameters. Field trials are conducted utilizing a 3-m vessel in a nearby estuary. Published