Little is known about how the Vulnerable dugong Dugong dugon uses coral reef lagoons despite the importance of these habitats throughout much of its vast range. We used GPS satellite tracking systems to explore the space use of 12 dugongs at 3 locations in the coral reef lagoons of the main island of New Caledonia in the southwest Pacific: Cap Goulvain, Ouano and Nouméa. The movements of the tracked dugongs varied among individuals and all except one animal undertook large-scale movements (>15 km; mean [±SE] 37.7 ± 5.2 km) from their capture location (maximum waterway distance range: 13.8 to 72.9 km). The straight-line distances between the furthest GPS locations during each animal’s tracking period ranged from 21.3 to 74.5 km. We identified areas used intensively by dugongs in all 3 study areas, some of which were areas where seagrass presence has not been verified, or where dugongs have not been observed during past aerial surveys. Dugongs spent most of their tracking time within the lagoons, with 99.4% of GPS locations found inside the barrier reef. Nonetheless, where the lagoon was narrow and confined, 3 tracked dugongs used the fore reef shelf outside the barrier reef in the open ocean to commute between bays. Our findings can inform conservation and management initiatives in New Caledonia as well as other countries within the dugong’s range which have similar habitat geomorphology but where dugongs occur in numbers too low to be tracked and are considered Critically Endangered.