Abstract Identifying the diverse assemblage of species inhabiting rocky and coral reef habitats in isolated oceanic environments, and the important sound cues emitted from the reef, are crucial components to understand how species locate suitable habitats for the completion of their life‐cycle and, thus, the functioning of these vulnerable ecosystems. Recent field information suggests that the majority of reef biodiversity comprises small cryptic invertebrates; however, knowledge on these small components is extremely scarce. The present study used light attraction methods to explore the diversity of larval, post‐larval and macrobenthic cryptic fauna, and hydrophones to characterize the natural soundscape of rocky and coral reef habitats at the Robinson Crusoe island (Juan Fernandez Archipelago; 33°38′S, 78°50′W), and Rapa Nui (Easter Island; 27°7′S, 109°21′W), respectively. Pelagic collections found important site‐specific patterns and identified two main species assemblages: early‐life stages (e.g. eggs, larval and juvenile stages of crustaceans, molluscs, and fishes) and emerging macrobenthos (e.g. demersal zooplankton such as peracarid crustaceans, ostracods, copepods, and polychaetes), with the latter contributing between 73 and 98% to the total catches. The soundscape records showed marked differences among sites and seasons at Robinson Crusoe island, with variable differences found between day and night. However, at Rapa Nui, there were no differences between sites, but the ambient sound was higher at night possibly due to higher snapping shrimp activity. This information highlights the importance of considering small‐scale (site‐to‐site) patterns when evaluating overlooked components of diversity (i.e. biological or acoustic) in oceanic habitats, and provides the basis for understanding the importance of natural noise in the settlement of most reef‐associated species, crucial features for the conservation of these remote and vulnerable ecosystems.