The work presented in this dissertation focuses on the paleoceanography of the Indonesian Seas over the past 25,000 years; a region that plays a critical role in the global atmospheric and oceanic circulation. The modern oceanography of the Indonesian Seas is very complex due to the combined impact of the East Asian Monsoon, the Australian Monsoon, the migration of the Inter-Tropical Convergence Zone (ITCZ) and the El Niño Southern Oscillation, which is reflected in sea surface temperature (SST) and salinity (SSS) changes in this region on both intra- and interannual timescales. Therefore, in order to explore the impacts of these various climate systems on the paleoceanography of the Indonesian Seas, unbiased estimates of past SST/ SSS are needed. One of the most common technique to infer past changes in SST is the measurement of Mg/Ca in the planktonic foraminifer Globigeriniodes ruber (white). When combined with the stable oxygen isotope (δ18O) measurements on the same foraminiferal sample, this technique allows to reconstruct past changes in δ18Osw, which varies linearly with SSS. This method assumes that the primary control on foraminiferal Mg/Ca is temperature, although several studies have shown that salinity can play an important role in the assimilation of Mg into biogenic calcite. Here I use foraminiferal Mg/Ca measurements from 165 core-top and sediment trap data with a global geographic distribution to show (1) that the Mg/Ca sensitivity to temperature is less than previously estimated (6%/°C vs 9%/°C) and (2) that although the effect of salinity on foraminiferal Mg/Ca is small between 32psu and 37psu (6%/psu), it needs to be taken into consideration to derive unbiased sea surface temperature and salinity estimates, especially on glacial/interglacial timescale. I propose a new set of calibration equations for estimating sea surface temperature and salinity in the 15-30°C/32-37psu range based on the paired measurements of Mg/Ca and δ18Oc on the same foraminiferal sample, which apply to the Indonesian Seas on glacial/interglacial timescales. These equations are then applied to eight published records from this region spanning the past 25,000 years. The unbiased estimates suggest a 4-4.5°C cooling in this region at the Last Glacial Maximum (LGM) as opposed to 2.5-3°C inferred from traditional Mg/Ca calibration equations. This cooling was accompanied by a region-wide local freshening, consistent with a more southerly position of the ITCZ and enhanced transport of 18O-depleted moisture from the Atlantic at the LGM. The record also suggests the presence of a temperature oscillation of ∼0.3-0.5°C during the deglaciation, coincident with the Northern Hemisphere Bølling-Allerød/Younger Dryas. This millennial temperature oscillation is accompanied by salinity changes, coincident with a change in the intensity of the summer East Asian Monsoon. SSSs reached a maximum in the early Holocene, supporting the hypothesis of a westward repositioning/expansion of the Western Pacific Warm Pool. SSSs then decreased over the Holocene, an observation consistent with a southerly displacement of the ITCZ. The flooding of the Sunda Shelf and the re-establishment of the “freshwater plug” in the southern Makassar Strait at 9.5ky B.P. is apparent in the SSS record, although there is no definite evidence for associated changes in heat transport from the Pacific to the Indian Ocean from the SST records. The Holocene has experienced several episodes of warming, culminating to the present warming trend. The last climate oscillation is the so-called Medieval Climate Anomaly/Little Ice Age (MCA/LIA). In order to investigate the hydrographic variability associated with the East Asian Monsoon, the relative mean position of the ITCZ and ENSO over this time interval, five high-resolution SST/SSS records from different locations within the Indonesian Seas are compared. The results suggest that hydrographic variability in this region was strongly associated with the MCA/LIA climate oscillation. Taken together, the records indicate a ∼0.5-1°C temperature change between the MCA and LIA. One of the records also indicates that, on average, the MCA was cooler than the 20th century, although several decades during the MCA show a warming comparable to that of the 20th century. The results also indicate a strengthening (weakening) of the East Asian Monsoon over the MCA (LIA), coincident with a northward (southward) migration of the ITCZ. However, the results do not indicate a preponderant role for ENSO in controlling the surface hydrographic variability found in this region over the past 2,000 years. In order to investigate the behavior of ENSO over the MCA/LIA, I used the stable isotope values of individual specimens of the thermocline-dwelling planktonic foraminifer Pulleniatina obliquiloculata from a sediment core collected from the Northern Makassar Strait. At this location, the δ18Oc produced by this foraminifer reflect the temperature and salinity variability that accompanies both eastern as well as central Pacific types of ENSO. Changes in ENSO strength/ frequency were estimated by comparing the spread and symmetry of δ18Ocalcite values extracted from discrete time horizons in this sediment core. The spread of individual δ18Ocalcite values is interpreted to be a measure of the strength of both phases of ENSO while the symmetry of the δ18Ocalcite distributions is used to evaluate the relative strength/frequency of El Niño and La Niña events. In contrast to previous studies, robust and resistant statistics were used to quantify the spread and symmetry of the δ18Ocalcite distributions; an approach motivated by the relatively small sample size and the presence of outliers. The results indicate that ENSO has remained remarkably constant over the past millennium, with no systematic difference between the relatively warm conditions of the MCA and the cool conditions of the LIA. However, the MCA was characterized by stronger/more frequent La Niña than El Niño; an observation consistent with the medieval megadroughts documented from sites in western North America.