A system that can be used for inspecting underwater structures. The system allows a user to gain a better understanding of the condition of an underwater structure. The system is a self-contained, modular system that can be operated by divers, coupled to an AUV, ROV or other host platform vehicle deployment platform, towed by a ship, pole mounted, or hull mounted. All of the components necessary to achieve the desired scanning functions are incorporated onto the self-contained, modular system. The system can include and fully utilize a 3D sonar system and an inertial navigation system. This combination of features permits the system to be used to, for example, generate 3D models of underwater structures, detect changes in underwater structures by comparing the generated 3D model against an a priori 3D model, and provide navigational updates to the host platform based on the observed features of an underwater structure.