We use a multiproxy approach to monitor changes in the vertical profile of the Indonesian Throughflow as well as monsoonal wind and precipitation patterns in the Timor Sea on glacial-interglacial, precessional, and suborbital timescales. We focus on an interval of extreme climate change and sea level variation: marine isotope (MIS) 6 to MIS 5e. Paleoproductivity fluctuations in the Timor Sea follow a precessional beat related to the intensity of the Australian (NW) monsoon. Paired Mg/Ca and δ18O measurements of surface- and thermocline-dwelling planktonic foraminifers (G. ruber and P. obliquiloculata) indicate an increase of >4°C in both surface and thermocline water temperatures during Termination II. Tropical sea surface temperature changed synchronously with ice volume (benthic δ18O) during deglaciation, implying a direct coupling of high- and low-latitude climate via atmospheric and/or upper ocean circulation. Substantial cooling and freshening of thermocline waters occurred toward the end of Termination II and during MIS 5e, indicating a change in the vertical profile of the Indonesian Throughflow from surface- to thermocline-dominated flow.