Dispersal patterns shape species’ distribution, abundance and persistence, their potential for genetic drift and adaptation, and ultimately determine rates of recovery following disturbances. Because the larval mortality and competency dynamics of most marine organism is altered under warmer conditions, it is fundamental to understand how climate change will alter current connectivity patterns. Here we used an experimentally calibrated high resolution unstructured-mesh, depth-integrated hydrodynamic model (SLIM) to project current and climate change-mediated dispersal and connectivity patterns of corals in the Great Barrier Reef (GBR). We show that as oceans warm, coral connectivity will decrease. Specifically, the average dispersal distance from origin to destination reef and the number of incoming connections to each reef decrease. Interestingly, the proportion of larvae that find a suitable place to settle increases because more larvae will settle in their natal reef. We also show that broadcast spawning species with greater egg sizes, such as Acropora spp., will experience greater changes in dispersal patterns than species with smaller eggs. We identified the reefs which contribute the most to the larval supply in the GBR and the reefs which recovery rates will be more affected by the change in connectivity patterns. Improved predictions of coral connectivity are essential to design networks of protected areas that contribute more effectively to the long-term sustainability and resilience of tropical reef ecosystems.