Movement of large marine predators can connect remote or isolated habitats and create links that are key for maintaining connectivity within and between ecosystems which is critical for understanding and mitigating the potential effects of their removal. We used a combination of acoustic telemetry data, network analysis, habitat modelling, and machine learning methods to quantify movement patterns and habitat use of three coral reef predators within and between two remote coral reef systems off North-West Australia. Grey reef sharks displayed greater movement than silvertip sharks and red bass, with connectivity linking distant reefs and atolls. Movement patterns and connectivity were more extensive at Rowley Shoals than at Scott Reef. Red bass movements resulted in local-scale connectivity between the lagoon and nearby forereef areas, whereas shark connectivity operated at broader scales, creating greater linkages across distant areas within the reef systems. Importantly, we show that existing spatial planning at these remote coral reefs is effective to protect local-scale movements of mesopredators, but that spatial protection at broader scales is still needed to effectively maintain the connectivity of large predators, which is crucial for the stability of isolated coral reef ecosystems.