This dataset contains fish counts on coral reefs, seagrass beds, and mangrove forests using a standardised surveying method. Surveys were conducted at three locations in the Caribbean (Grand Cayman, Bonaire, and St. Croix) and two on the Great Barrier Reef (the Palm Island and Lizard Island). The objective of collecting this data was to compare the overlap in fish assemblages between these habitats to ask if it differed depending on the realm (Caribbean and GBR). Furthermore, we assessed nursery function as the dataset contains fish counts segregated by two different size classes (> and < 10cm total length).