The pathways of the Pacific to Indian Ocean throughflow and the relative contributions of North Pacific (NP) and South Pacific (SP) water to the throughflow are examined using the Navy Layered Ocean Model. The roles of Halmahera Island in directing flow along the pathways and determining the composition of the throughflow are also studied. The global ocean simulations use a horizontal resolution of up to 1/4° between like variables and have a vertical resolution ranging from one and a half layer reduced gravity to six active layers with realistic bottom topography. All of the simulations are forced by the Hellerman and Rosenstein  monthly wind stress climatology. The predominant throughflow pathway consists of NP water traveling through the Celebes Sea, Makassar Strait, Flores Sea, and to the Indian Ocean through the Timor, Savu, and Lombok Straits. Model results show that the island of Halmahera is responsible for preventing a flow of SP water into the Celebes Sea and for diverting some SP water southward through the Seram and Banda Seas. The island impacts the lower thermocline and intermediate water pathways throughout the entire year and affects the surface layer during the boreal spring through fall. To estimate the relative contributions of the NP and SP surface water to the throughflow, Lagrangian drifters are advected backward in time from near the exit to the throughflow region to their respective sources. By tracking these buoys, it is found that the presence of Halmahera changes the throughflow composition in the surface layer from ∼69% NP and 31% SP to 92% NP and 8% SP. Halmahera does not change the composition of the throughflow in the undercurrent layer, which is fed by the NP, or in the lower thermocline and intermediate water layers, which are fed by water from the SP.