The three-dimensional climatological spreading of South Pacific waters over the Maritime Continent is examined using eddy-resolving simulations and a passive tracer method. Four pathways are summarized for the South Pacific Tropical Water and the Antarctic Intermediate Water through the Maritime Continent, including two direct pathways, namely, the Eastern Path and the Torres Strait Path, and two indirect pathways, namely, the Western Path and the South China Sea Path. Among them, according to tracer concentration distribution, the former two contribute most of the volume transport of the Indonesian Throughflow (ITF) originating from the South Pacific. The latter two experience two retroflections (i.e., the South Equatorial Current-Equatorial Undercurrent and the North Equatorial Countercurrent-North Equatorial Current) before entering the Indonesian Seas. The vertical distributions of the South Pacific waters along each path throughout the Indonesian Seas are also analyzed, revealing that the South Pacific salinity extrema greatly affect the intermediate and deep layers of the Indonesian Seas and ITF as well as the upper thermocline. Vertical fluxes, especially vertical advection, are vital to these Indo-Pacific water exchange processes. Sensitivity tests are conducted for the vertical diffusion coefficient and initial conditions, the results of which are robust. According to current study, the South Pacific has substantial impacts on the water properties throughout the Maritime Continent and the mass-energy exchanges between the Pacific and Indian Oceans.