The ocean circulation in the Greater Great Barrier Reef (GBR) region is influenced by the basin-scale ocean circulation, especially the East Australian Current and the Gulf of Papua Current, which result from the bifurcation of the South Equatorial Current (SEC) when it reaches the Australian continental shelf. The SEC bifurcation latitude marks the division of the warm tropical gyre and cool subtropical gyre at the western boundary. Several studies have shown that there is a long-term southward shift of the SEC bifurcation latitude over the last 60 years. In this study the future changes in ocean circulation in the Great Barrier Reef are investigated using a high-resolution ocean model, forced with CMIP5 multi-model-mean climate change signals under the greenhouse gas concentration trajectory of Representative Concentration Pathway 8.5 (RCP8.5). We show that the SEC bifurcation continues shifting southward for the next 100 years; and we investigate its implications for the physical connectivity in the GBR region and explore how the health of marine ecosystems will be impacted.