Tropical inter-reefs represent a vast overlooked marine ecosystem that occurs between coral reefs and across the shelf. We deployed 60 baited remote underwater video stations (BRUVS) in New Caledonia to study inter-reef fish assemblages and habitats in three zones (bays, sandy lagoons, and sandy areas near the barrier reef) along an inshore-offshore gradient. Inter-reef habitats were dominated by soft bottoms with 83-98% of sand, and difference between the three zones was mainly driven by more sparse coral and macroalgae near the barrier reef. Overall, 148 fish species were recorded, and rarefaction curves extrapolated between 200 and 300 species on inter-reefs. Permutational linear models showed an increasing gradient in fish richness and abundance from the bays to the sand flats near the barrier reef with weak effect of individual habitat features. Two main fish assemblages were distinguished pertaining to an inshore and offshore cluster. While this structure partially followed the three inshore-offshore zones with distinct benthic habitat composition, it highlights that the largest ecosystem of the lagoon is dominated by commercial species. Our results using a low sampling size seem consistent with historical studies. BRUVS remain non-destructive and easy to deploy, making them a potentially good tool to study fish in marine tropical lagoons and should have applications for fishery management and conservation planning.