Abstract The vertical structure of the exchange of water between the Pacific and Indian Oceans via the Indonesian throughflow and its temporal variability are examined. Since there are no simultaneous, direct observations of transport variations with depth at the inflow straits (Makassar, Maluku, and Halmahera) and outflow straits (Lombok, Ombai, and Timor), numerical model results are used. Analysis of depth-integrated transport through the model straits indicates differences in the vertical structure of the flow between the inflow and outflow straits. Generally speaking, local winds affect flow in a layer above the thermocline, while remote forcing, e.g., ENSO or coastal Kelvin waves, affect flow in a subsurface layer. On the outflow side, transport occurs primarily in two vertical modes. The dominant mode is characterized by a surface intensification that decays to zero around 400 m . The second mode is characterized by flow in the upper 100 m that is of opposite direction to flow from 100 to 400 m . The vertical decomposition of transport through the model's inflow straits varies between the straits. At Makassar, the western-most inflow passage, the dominant mode is similar to the outflow straits, with a surface intensification of southward transport that decays to zero at 800 m . At Halmahera, the eastern-most inflow strait, the dominant mode is two-layer, with surface to 200 m transport in the opposite direction of transport from 200 to 700 m , similar to the second mode at the outflow straits. At Maluku, the center inflow passage, the dominant vertical mode is three-layer. At this strait, there is a layer from about 100 to 800 m within which flow is in the opposite direction to flow in a surface layer above 100 m and in a deeper layer below 800 m . Phase lags on the annual cycle suggest that during April–October, peaking in May, there is a convergence of mass in the upper 100 m of the Indonesian seas. This convergence is balanced by a mass divergence from 100 to 710 m that occurs slightly earlier but is of shorter duration, from February to mid-June. While interannual variations of transport in the straits varies, the difference in inflow and outflow on interannual timescales is correlated to ENSO. There is a divergence (convergence) of mass in the upper 100 m (100– 710 m ) in the Indonesian seas during the El Ninos of 1982/1983, 1986/1987, 1994/1995 and 1997/1998.