The inspection of aquatic environments is a challenging activity, which is made more difficult if the environment is complex or confined, such as those that are found in nuclear storage facilities and accident sites, marinas and boatyards, liquid storage tanks, or flooded tunnels and sewers. Human inspections of these environments are often dangerous or infeasible, so remote inspection using unmanned underwater vehicles (UUVs) is used. Due to access restrictions and environmental limitations, such as low illumination levels, turbidity, and a lack of salient features, traditional localisation systems that have been developed for use in large bodies of water cannot be used. This means that UUV capabilities are severely restricted to manually controlled low-quality visual inspections, generating non-geospatially located data. The localisation of UUVs in these environments would enable the autonomous behaviour and the development of accurate maps. This article presents a review of the state-of-the-art in localisation technologies for these environments and identifies areas of future research to overcome the challenges posed.