This study addresses the detailed modeling and simulation of the dynamic coupling between an underwater vehicle and manipulator system. The dynamic coupling effects due to damping, restoring, and inertial effects of an underwater manipulator mounted on an autonomous underwater vehicle (AUV) are analyzed by considering the actuator and sensor characteristics. A model reference control (MRC) scheme is proposed for the underwater vehicle-manipulator system (UVMS). The effectiveness of the proposed control scheme is demonstrated using numerical simulations along with comparative study between conventional proportional-integral-derivative (PID) control. The robustness of the proposed control scheme is also illustrated in the presence of external disturbances and parameter uncertainties. © 2013 Mohan Santhakumar.