Seasonal transport variations between the Pacific and Indian Oceans via the Indonesian seas were studied by the Euler-Lagrangian method. The velocity field was calculated with a fairly high resolution robust diagnostic model. The model well reproduces the features of seasonal variations in the Indonesian seas. The total volume transport of the Indonesian throughflow is 20±3 Sv (1 Sv = 106 m3 s−1), the maximum being from boreal spring to boreal summer and the minimum in boreal winter. The values are similar to those of previous general circulation models with a wide Indonesian passage despite resolution of the presence of the many small islands in the Indonesian seas. Although a large portion of the net transport is contained in the upper layer, deep transport below 1000-m depth is about 5 Sv. This value corresponds to approximately 25% of the total transport, which means that disregard of the deep transport leads to underestimation of the volume transport of the throughflow. Tracking of numerous labeled particles in the calculated velocity field clarified the sources and pathways of the Indonesian throughflow. The major route is a western one through both the Makassar and Lombok Straits. Most of the North Pacific water supplied from the Mindanao Current passes along this route, entering the Indian Ocean within several months with almost no loss of its properties (intense vertical mixing around the Lombok sill reported by observations could not be reproduced in our model). In contrast, South Pacific water takes the eastern route into the eastern Indonesian seas and subsequently mixes with waters from the North Pacific and Indian Oceans in the Banda Sea, which means that it has a long travel time (at least a few years). Water taking the eastern route therefore loses its original properties before arriving in the Indian Ocean. The transport processes also are significantly affected by seasonal variations in equatorial circulation in the western Pacific. In the surface layer, North Pacific water is vigorously supplied to the western route only from boreal spring to summer in association with the linkage between the current flowing through the Makassar Strait and the Mindanao Current. In other seasons, because the Mindanao Current is strongly linked with the North Equatorial Countercurrent and the New Guinea Coastal Current primarily by northeasterly monsoonal winds, its upper water flows back to the Pacific Ocean. In the subsurface layer, a pronounced inflow of Mindanao Current water into the western route occurs from boreal winter to spring, when the subsurface link between that current and the Equatorial Undercurrent tends to weaken. In the deep, the quasi-steady transport of Pacific water into the Indian Ocean via the eastern route is fed by the westward deep current in the equatorial Pacific.