<p>Coastal ecosystems, composed of mangroves, seagrass beds, and coral reefs, are intricately interconnected and play a critical role in maintaining marine biodiversity, particularly as important nursery habitats for juvenile reef fish. The nursery hypothesis suggests that mangroves and seagrass beds are vital during the transition of reef fish from juvenile to adult stages. However, debates regarding the significance of these habitats persist, especially in the Indo-Pacific region, where the relative contributions of mangroves and seagrass beds to reef fish populations remain underexplored. Advances in methodologies such as underwater visual census, biological tagging, stable isotope analysis, and population genetics have provided valuable insights into fish connectivity and habitat functionality. Despite challenges in identifying nursery habitats, ongoing research has deepened our understanding by examining factors like predation risk, food availability, and genetic connectivity. Collaborative research efforts and long-term monitoring programs are crucial for capturing global variability and effectively addressing conservation challenges. By employing interdisciplinary approaches and technological innovations, future studies promise to enhance our understanding of coastal ecosystems and support sustainable management practices. This review synthesizes current research on the connectivity of fish assemblages among mangroves, seagrass beds, and coral reefs, highlights the ecological dynamics underpinning these habitats, examines the ongoing debates surrounding the nursery habitat concept, and identifies key research directions. By adopting interdisciplinary approaches and implementing long-term monitoring, future research can refine our understanding of coastal ecosystems, support biodiversity conservation, and inform sustainable strategies to mitigate increasing anthropogenic and climate pressures.</p>