Since Last Glacial Maximum (23–19 ka), Earth climate warming and deglaciation occurred in two major steps (Bølling-Allerød and Preboreal), interrupted by a short cooling interval referred to as the Younger Dryas (12.5–11.5 ka B.P.). In this study, three cores (MV-33, MV-66, and MD-40) collected in the central part of Pandora Trough (Gulf of Papua) have been analyzed, and they reveal a detailed sedimentary pattern at millennial timescale. Siliciclastic turbidites disappeared during the Bølling-Allerød and Preboreal intervals to systematically reoccur during the Younger Dryas interval. Subsequent to the final disappearance of the siliciclastic turbidites a calciturbidite occurred during meltwater pulse 1B. The Holocene interval was characterized by a lack of siliciclastic turbidites, relatively high carbonate content, and fine bank-derived aragonitic sediment. The observed millennial timescale sedimentary variability can be explained by sea level fluctuations. During the Last Glacial Maximum, siliciclastic turbidites were numerous when the lowstand coastal system was located along the modern shelf edge. Although they did not occur during the intervals of maximum flooding of the shelf (during meltwater pulses 1A and 1B), siliciclastic turbidites reappear briefly during the Younger Dryas, an interval when sea level rise slowed, stopped, or perhaps even fell. The timing of the calciturbidite coincides with the first reflooding of Eastern Fields Reef, an atoll that remained exposed for most of the glacial stages.