The Mozambique Channel is a conduit of trade wind-driven, warm and salty throughflow that is a key component of the Agulhas Current and Agulhas leakage. Agulhas leakage is a flux of warm and salty water from the tropical Indian to the Atlantic Ocean and is thought to strengthen the Atlantic meridional overturning circulation (AMOC). Previous studies from the Agulhas region suggest that enhanced Agulhas leakage, driven by shift and intensification of the southern hemisphere westerlies, played an important role in accelerating glacial terminations. The southeastern monsoon response to freshwater-induced climate instabilities that punctuated the last deglaciation and its impact on the Mozambique Channel through flow and, by extension, on the Agulhas leakage is not well understood. Here we present a high-resolution hydroclimate and mixed layer temperature reconstruction using three sediment cores collected from the runoff-influenced eastern Mozambique Channel, off northwestern Madagascar, in the core region of the southern hemisphere monsoon domain. Local δ18O seawater time-series, obtained by removing the calcification temperature and ice volume imprints on δ18O of Globigerinoides ruber tests, is used as a proxy of river runoff and, by extension, precipitation changes over northwestern Madagascar. Superimposed on orbital scale climate trend that indicates a humid glacial, the proxy record reveals precipitation increases centered at 11-13 thousand years before present (kyr BP), 14-18 kyr BP, and 23-25 kyr BP. Considering age model uncertainty, this is the first strong and consistent evidence for southern African monsoon strengthening in response to freshwater forcing during Younger Dryas (YD), Heinrich Event 1 (H1), and Heinrich Event 2 (H2). Furthermore, our study shows a reversal of mixed layer temperature gradient between the west and east Mozambique Channel during H1 and YD. Consistent with the results of climate simulation, we suggest that the gradient reversal indicates a weakening of the trade wind-driven South Equatorial Current and Mozambique Channel throughflow that weakens the Agulhas leakage. In conclusion, the results of this study indicate that millennial scale weakening of Mozambique Channel through flow is strongly linked to the changes in the southern hemisphere monsoon wind fields over the Tropical Indian Ocean. As shown in this study, the latter is sensitive to northern high latitude freshwater forcing, potential creating a positive feedback that contributes to the weakening of the AMOC by reducing the amount of heat and salt leakage into the Atlantic.