Development of underwater vehicles (UVs) has come to an era that UVs can be specifically designed and made for customized applications, based on established theories and principles. This paper reports on the Canterbury UV developed at the University of Canterbury, which targets to inspect and clean sea chests of ships to eliminate bio-security risks caused by small organisms residing in the sea chests. Based on the mechanical prototype, navigation of the Canterbury UV is discussed in principle with the aim to providing theoretical ground for the future implementation of navigation control. Simulation results of the UV model demonstrate that the vehicle can be controlled with satisfying performance using the extended Kalman filter.