The upper ocean circulation of the Pacific and Indian Oceans is connected through both the Indonesian Throughflow north of Australia and the Tasman leakage around its south. The relative importance of these two pathways is examined using virtual Lagrangian particles in a high-resolution nested ocean model. The unprecedented combination of a long integration time within an eddy-permitting ocean model simulation allows the first assessment of the interannual variability of these pathways in a realistic setting. The mean Indonesian Throughflow, as diagnosed by the particles, is 14.3 Sv, considerably higher than the diagnosed average Tasman leakage of 4.2 Sv. The time series of Indonesian Throughflow agrees well with the Eulerian transport through the major Indonesian Passages, validating the Lagrangian approach using transport-tagged particles. While the Indonesian Throughflow is mainly associated with upper ocean pathways, the Tasman leakage is concentrated in the 400–900 m depth range at subtropical latitudes. Over the effective period considered (1968–1994), no apparent relationship is found between the Tasman leakage and Indonesian Throughflow. However, the Indonesian Throughflow transport correlates with ENSO. During strong La Niñas, more water of Southern Hemisphere origin flows through Makassar, Moluccas, Ombai, and Timor Straits, but less through Moluccas Strait. In general, each strait responds differently to ENSO, highlighting the complex nature of the ENSO-ITF interaction.