Presented at the 2018 AGU Fall MeetingThe Maritime Continent (MC) offers the only low-latitude connection of the world oceans. The oceanography within the MC regulate the characteristics of the Indonesian throughflow (ITF), linking the tropical Pacific and Indian Oceans, with strong implications to climate variability and biogeochemistry. Previous studies suggested that the relatively fresh South China Sea (SCS) waters advected by the monsoonal wind-driven ocean currents create an upper-layer "freshwater plug" in the Java Sea and Makassar Strait during boreal winter, which modulates the vertical structure and variability of the ITF. Using a suite of satellite observations to characterize the freshwater plug and examine its sources, we find that the main source of the freshwater is derived directly from the Java Sea precipitation and the Kalimantan(Borneo) rivers. The freshwater plug not only occurs in boreal winter but persists into boreal spring. The boreal-winter monsoonal precipitation over the Java Sea is a major source for the freshwater plug. Runoff from Kalimantan caused by the boreal winter-spring precipitation re-enforces and prolongs the freshwater plug into boreal spring. The boreal winter-spring freshening is associated with a northward decrease of sea level anomaly in the Makassar Strait, reflecting the impact on the ITF. Therefore, the monsoonal water cycle in the MC plays a critical role in regulating the low-latitude chokepoint of global ocean circulation seasonally. The results also have implications to ITF variations and the related impacts associated with longer-term changes of Indo-Pacific climate variability and water cycle in the MC region.