The Indonesian throughflow is analyzed in an extended simulation with a coupled ocean-atmosphere model. The model, developed by the Max-Planck-Institut für Meteorologie, Hamburg, Germany, combines an atmospheric general circulation model at T42 resolution (2.8° latitude by 2.8° longitude) and a primitive equation ocean model with zonal resolution of 2.8° and a meridional resolution of 0.5° in the tropics and is coupled without flux correction equatorward of a latitude of 60°. The onset and strength of the monsoon in the Indonesian waters agree well with climatology, and many aspects of the observed temperature fields in the eastern Indian Ocean and Timor Seas are found in simulation. Differences between simulation and observations of temperature occur in mean and seasonal cycles in the far western Pacific. The annual cycles of sea level along the coast of Sumatra and Java are simulated satisfactorily. The simulated throughflow transports on average 13.8 Sv (106m3S−1) from the Pacific to the Indian Ocean. The vertically averaged (barotropic) component of the throughflow has a seasonal range of 13.1 Sv and is weakest in February and strongest in July. In contrast, deviations from the vertical average of the throughflow (baroclinic) are strongest in March and September. The average and seasonal cycle of the barotropic component of the throughflow are forced by winds over the Pacific and along the western coasts of Australia and South America, as described by the island rule. For closed Torres Strait, the contribution of the average bottom pressure torque is small, and friction closes the vorticity balance. For annual timescales, baroclinic flows affect the throughflow transport through the bottom pressure torque. The annual cycle of the baroclinic component of the throughflow is forced predominantly by winds over the Indonesian Seas. The throughflow exports 0.9 PW of heat from the Pacific into the Indian Ocean and is an important heat sink for the western Pacific. The throughflow is a major heat source for the Indian Ocean and is associated with reversal of the divergence of the meridional transport of heat south of 10°S that is balanced by heat fluxes from the ocean to the atmosphere.