A 1/12° global version of the HYbrid Coordinate Ocean Model (HYCOM) using 3-hourly atmospheric forcing is analyzed and directly compared against observations from the International Nusantara STratification ANd Transport (INSTANT) program that provides the first long-term (2004–2006) comprehensive view of the Indonesian Throughflow (ITF) inflow/outflow and establishes an important benchmark for inter-basin exchange, including the net throughflow transport. The simulated total ITF transport (−13.4 Sv) is similar to the observational estimate (−15.0 Sv) and correctly distributed among the three outflow passages (Lombok Strait, Ombai Strait and Timor Passage). Makassar Strait carries ∼75% of the observed total ITF inflow and while the temporal variability of the simulated transport has high correlation with the observations, the simulated mean volume transport is ∼37% too low. This points to an incorrect partitioning between the western and eastern inflow routes in the model and is the largest shortcoming of this simulation. HYCOM simulates the very deep (>1250 m) overflow at Lifamatola Passage (−2.0 Sv simulated vs. −2.5 Sv observed) and indicates overflow contributions originating from the North (South) Equatorial Current in boreal winter–spring (summer–autumn). A new finding of INSTANT is the mean eastward flow from the Indian Ocean toward the interior Indonesian Seas on the north side of Ombai Strait. This flow is not robustly simulated at 1/12° resolution, but is found in a 1/25° version of global HYCOM using climatological forcing, indicating the importance of horizontal resolution. However, the 1/25° model also indicates that the mean eastward flow retroflects, turning back into the main southwestward Ombai Strait outflow, and in the mean does not enter the interior seas to become part of the water mass transformation process. The 1/12° global HYCOM is also used to fill in the gaps not measured as part of the INSTANT observational network. It indicates the wide and shallow Java and Arafura Seas carry −0.8 Sv of inflow and that the three major outflow passages capture nearly all the total Pacific to Indian Ocean throughflow.