The eastern tropical Indian Ocean (ETIO) off southern Indonesia is a very important region for the global thermohaline circulation as it hosts the exit pathway of the Indonesian Throughflow (ITF). From this region cool and fresh ITF waters are advected by the South Equatorial Current (SEC) to the Indian Ocean. Consequently, the ITF water freshens the Indian Ocean. Nevertheless, the hydrology condition was different during the Last Glacial Maximum (LGM). During this period the sea level was low and the Sunda Shelf was an exposed land. Marine records and simulation study suggest that the exposure of the Sunda Shelf caused a significant reduction in convection over the Indonesian region, resulting arid condition and saltier sea surface condition off south Java. Armed with two sedimentary archives collected from the ETIO off the Sunda Strait, this dissertation investigates the evolution of hydrological changes in the ETIO during the past ~40 kyr B.P. with respect to the flooding of the Sunda Shelf. Furthermore, this dissertation examines the applicability of planktic foraminifera Ba/Ca ratio as a tracer for freshwater discharge. New results of Mg/Ca-based sea surface temperature (SST), seawater à ´18O (à ´18Osw), and XRF-Ti/Ca ratio of GeoB 10042-1 and GeoB 10043-3 collected from off the Sunda Strait revealed that the region has experienced prominent hydrological changes during the past ~40 kyr B.P. The results show that sea surface conditions off the Sunda Strait were cooler and saltier conditions during the last glacial compared to the Holocene, and support previous finding that suggests slowdowns of the Atlantic meridional overturning circulation (AMOC) during the Heinrich stadials 1-3 and the Younger Dryas have caused dry conditions in the ETIO region. Whereas during the Holocene sea surface conditions off the Sunda Strait exhibit warmer and fresher conditions, particularly after the opening of the Sunda Strait at ~10 kyr B.P. This fresher sea surface condition is maintained until today as a consequence of persistent transport of low salinity Java Sea water into the ETIO via the Sunda Strait. Novel millennial-scale reconstruction of past bottom water conditions (foraminifera à µNd) show distinct modifications of the bottom water (2171 m) off the Sunda Strait during the past 19 kyr. Modifications of the bottom water during the last deglaciation and the Holocene correspond to a strong- and a weak thermocline ITF flow, respectively. Furthermore, the results imply that the variability of the detrital à µNd data off the Sunda Strait is susceptible to the ITF flow and large terrigenous material supply from the Sunda Strait. Planktic foraminifera Ba/Ca ratio has been recently used to reconstruct modern and past freshwater discharge. The application of this proxy is based on the observation that suggests that the Ba/Ca ratio of seawater is directly incorporated into foraminifera calcite, and river water has a distinctly higher Ba/Ca ratio than seawater. However, cleaning experiments results on planktic foraminifera G. sacculifer collected from the ETIO revealed that the Ba/Ca ratio of G. sacculifer cannot be used as a tracer for modern and past salinity changes due to the appearance of seasonal upwelling complicates the interpretation of the proxy.