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Abstract: Tectonic changes of the Early to Mid-Pliocene largely modified the Indonesian Passages by constricting and uplifting the passages between today''s New Guinea and Sulawesi. The associated changes in strength and water mass properties of the Indonesian throughflow (ITF) might have influenced the amount of heat transported from the Pacific to the Indian Ocean and thus contributed to Pliocene climate change of the Indo-Pacific. We study the climate response to changes in the geometry of the Indonesian Passages in an atmosphere–ocean general circulation model (AOGCM). We compare climate simulations with present-day topography and with a topography resembling the Early Pliocene situation in the Indo-Pacific, i.e. passages East of Sulawesi deepened and widened to the South. We find that transport through the Indonesian Archipelago is weakened in the constricted passage by 1.7Sv and in the unchanged Makassar Strait West of Sulawesi by 3.5Sv, while transport weighted temperature of the outflow into the Indian Ocean increases by 1°C. Consistent with recent proxy evidence the reduction in ITF transport causes a decrease in subsurface temperatures in the Indian Ocean while surface waters of the equatorial Pacific exhibit an increase by up to 0.9°C centred in the warm pool. As a local response to the sea surface temperature anomalies, we observe an anomalous precipitation dipole across the Indonesian passages with increased rainfall over the Pacific warm pool and decreased precipitation in the eastern Indian Ocean. The Australian continent experiences a pronounced aridification with mean annual precipitation rates dropping by 30% over most parts of the continent. Using an uncoupled vegetation model, we demonstrate that the simulated climate change might partly explain the observed Late Pliocene desertification of Australia. [Copyright &y& Elsevier]