Western Pacific central and tropical waters characterized by a subsurface salinity maximum spread into the Indonesian seas as part of the Indonesian throughflow. Within the Indonesian seas this salinity maximum is attenuated and, in some places, completely removed. A simple advection-diffusion model verifies the importance of vertical mixing in the transformation of Western Pacific waters to Indonesian thermocline water. The profiles indicate a predominant North Pacific presence in most of the seas, although some South Pacific water is present in the eastern ses of Halmahera, Seram, and Banda. The main interocean route is through the western seas of Sulawesi, Makassar, and Flores, while the flow pathway in the eastern seas is less certain. The Banda Sea can be renewed from either the northern passages (Halmahera and Maluku) or from the south via the Flores Sea. Using representative basin property profiles derived from the archieved data allows determination of a range of vertical diffusivities an... Abstract Western Pacific central and tropical waters characterized by a subsurface salinity maximum spread into the Indonesian seas as part of the Indonesian throughflow. Within the Indonesian seas this salinity maximum is attenuated and, in some places, completely removed. A simple advection-diffusion model verifies the importance of vertical mixing in the transformation of Western Pacific waters to Indonesian thermocline water. The profiles indicate a predominant North Pacific presence in most of the seas, although some South Pacific water is present in the eastern ses of Halmahera, Seram, and Banda. The main interocean route is through the western seas of Sulawesi, Makassar, and Flores, while the flow pathway in the eastern seas is less certain. The Banda Sea can be renewed from either the northern passages (Halmahera and Maluku) or from the south via the Flores Sea. Using representative basin property profiles derived from the archieved data allows determination of a range of vertical diffusivities an...