The Coral Sea houses expansive coral reefs. Reef health is inextricably linked to water temperatures, which are regulated by the hydrodynamic environment. The current system in the Coral Sea is dominated by jets of the South Equatorial Current (SEC): the North Vanuatu Jet (NVJ), the North Caledonian Jet (NCJ) and the South Caledonian Jet (SCJ). We investigated the projected near-future (2050) changes in the temperature and transport structure of the Coral Sea. We utilized the three highest resolution climate models from the CMIP6 HighResMIP experiment as these models broadly captured the historical temperature and transport structure of the SEC jets, and their El Niño Southern Oscillation (ENSO) related variability. Surface warming of 0.78°C and 1.12°C was projected in the Coral Sea under 1.5°C and 2°C global warming, respectively. The warming signal deepened by 30 m per decade, penetrating to 400 m by 2050. This indicates the additional thermal stress that could be experienced by Coral Sea ecosystems with future global warming. Decreases in the transports of the NVJ and NCJ, and an intensification of the SCJ were projected in the HighResMIP models. While the magnitudes of the changes were relatively small (2% to 7% of historical means), they were similar to the variability in NVJ and NCJ transport associated with ENSO. Our analysis further shows that the transport projections of the NVJ and NCJ varied with depth, where surface intensifications coincided with the areas of greatest warming. These changes could modify upwelling dynamics on the Great Barrier Reef shelf.