Unmanned underwater vehicles (UUV) play an importation role in the exploration and exploitation of the deep sea environment. The requirement for accurate navigation systems for such vehicles is of vital importance to their feasibility. This paper discusses the development of a real time navigation system that takes advantage of the complimentary attributes of a sensor suite including a DVL, compass, depth sensor, altimeter sensor and a recently developed vision based motion estimation algorithm. Testing of newly developed vision based algorithms in real underwater environments poses many challenges. To tackle some of the problems involved in testing, details of the development of two novel means of vision based algorithm testing are presented; physical and virtual simulation. The paper also details the experimental setup for test tank trials utilizing a seabed poster representation, including results gained, as well as the experimental setup for sea trials of the University of Limerick’s newly developed thrusted pontoon/ROV.