Circulations associated with the Indonesian Throughflow (IT), particularly concerning subsurface currents in the Pacific Ocean, are studied using three types of models: a linear, continuously stratified (LCS) model and a nonlinear, 4 1 2 -layer model (LOM), both confined to the Indo-Pacific basin; and a global, ocean general circulation model (COCO). Solutions are wind forced, and obtained with both open and closed Indonesian passages. Layers 1–4 of LOM correspond to near-surface, thermocline, subthermocline (thermostad), and upper-intermediate (AAIW) water, respectively, and analogous layers are defined for COCO. The three models share a common dynamics. When the Indonesian passages are abruptly opened, barotropic and baroclinic waves radiate into the interiors of both oceans. The steady-state, barotropic flow field from the difference (open − closed) solution is an anticlockwise circulation around the perimeter of the southern Indian Ocean, with its meridional branches confined to the western boundaries of both oceans. In contrast, steady-state, baroclinic flows extend into the interiors of both basins, a consequence of damping of baroclinic waves by diapycnal processes (internal diffusion, upwelling and subduction, and convective overturning). Deep IT-associated currents are the subsurface parts of these baroclinic flows. In the Pacific, they tend to be directed eastward and poleward, extend throughout the basin, and are closed by upwelling in the eastern ocean and Subpolar Gyre. Smaller-scale aspects of their structure vary significantly among the models, depending on the nature of their diapycnal mixing. At the exit to the Indonesian Seas, the IT is highly surface trapped in all the models, with a prominent, deep core in the LCS model and in LOM. The separation into two cores is due to near-equatorial, eastward-flowing, subsurface currents in the Pacific Ocean, which drain layer 2 and layer 3 waters from the western ocean to supply water for the upwelling regions in the eastern ocean; indeed, depending on the strength and parameterization of vertical diffusion in the Pacific interior, the draining can be strong enough that layer 3 water flows from the Indian to Pacific Ocean. The IT in COCO lacks a significant deep core, likely because the model’s coarse bottom topography has no throughflow passage below 1000 m. Consistent with observations, water in the near-surface (deep) core comes mostly from the northern (southern) hemisphere, a consequence of the wind-driven circulation in the tropical North Pacific being mostly confined to the upper ocean; as a result, it causes the near-surface current along the New Guinea coast to retroflect eastward, but has little impact on the deeper New Guinea undercurrent. In the South Pacific, the IT-associated flow into the basin is spread roughly uniformly throughout all four layers, a consequence of downwelling processes in the Indian Ocean. The inflow first circulates around the Subtropical Gyre, and then bends northward at the Australian coast to flow to the equator within the western boundary currents. To allow for this additional, northward transport, the bifurcation latitude of the South Equatorial Current shifts southward when the Indonesian passages are open. The shift is greater at depth (layers 3 and 4), changing from about 14°S when the passages are closed to 19°S when they are open and, hence, accounting for the northward-flowing Great Barrier Reef Undercurrent in that latitude range. After flowing along the New Guinea coast, most waters in layers 1–3 bend offshore to join the North Equatorial Countercurrent, Equatorial Undercurrent, and southern Tsuchiya Jet, respectively, thereby ensuring that northern hemisphere waters contribute significantly to the IT. In contrast, much of the layer 4 water directly exits the basin via the IT, but some also flows into the subpolar North Pacific. Except for the direct layer 4 outflow, all other IT-associated waters circulate about the North Pacific before they finally enter the Indonesian Seas via the Mindanao Current.