An extensive series of numerical experiments using a non-linear, high-resolution ocean model centered over the Indonesian Seas are performed to investigate the fundamental dynamics of the Indonesian Seas Throughflow. The model is initialized with seasonally varying prescribed transports through four open ports that simulate the Pacific and Indian Ocean major currents. Atmospheric coupling is accomplished with local monthly wind stresses from the Hellerman and Rosenstein climatology. Results from the barotropic experiment with no wind forcing reveal that the Mindanao Current splits towards the Makassar Strait, the Malucca Sea, and the Halmahera Sea and exits via the Lombok, Sumba, Ombai Straits and the Timor Sea. Barotropic experiments with local wind forcing reveal that the majority of the Mindanao Current transport flows toward the North Pacific Ocean during the southeast boreal monsoon, and towards the Celebes Sea during the northwest boreal monsoon. Results from the baroclinic, high-resolution model with and without wind forcing will also be discussed.