The Underwater Prefab Shelter is a building unique to the Gungans. They function exactly like their Prefab Shelter counterparts, providing 5 population per shelter, with the exception that they are built in the water by Utility Trawlers. They are useful when a player's base runs out of space for regular Prefab Shelters, as few buildings are present in the vast oceans of most maps. They are completely useless on space maps, as Shipyards are not buildable on those kinds of maps.
- Underwater Prefab Shelters are inspired by the aquatic buildings in the city of Otoh Gunga, from The Phantom Menace.
- The Underwater Prefab Shelter is the only unique building in the game.