A water mass analysis of the Coral Sea thermocline waters provides a description of their distribution, pathways and mixture based on recent oceanographic cruises in this region of strong western boundary currents. The Optimum Multiparameter method is used to determine the relative contribution of core water masses based on their measured temperature, salinity and dissolved oxygen. The thermocline waters, carried by the broad South Equatorial Current (SEC), are essentially composed of four core water masses of different origins. Coming from the south, the South Pacific Tropical Water South (SPTWS, delta = 25.3 kg m−3) and the Western South Pacific Central Water (WSPCW, σ = 26.3 kg m−3) enter the Coral Sea by the channel between the island of New Caledonia and the Vanuatu archipelago. Coming from the north, the South Pacific Tropical Water North (SPTWN, σ = 24.5 kg m−3) and the Pacific Equatorial Water (PEW, σ = 26.3 kg m−3) flow north of Vanuatu. The upper thermocline water that exits the Coral Sea equatorward, is mainly composed of SPTWN carried by the New Guinea Coastal Undercurrent. In contrast, upper thermocline waters exiting the Coral Sea poleward, in the East Australian Current, is dominated by SPTWS. The relative contributions are different in the lower thermocline where WSPCW dominates both western boundary currents. This refined description is consistent with the dynamics of the main currents, with a very strong depth dependence in the partitioning of incoming SEC waters.