The Indonesian Seas provide an oceanic pathway, the Indonesian Throughflow (ITF) that transports heat and freshwater from the tropical Pacific Ocean into the Indian Ocean. The ITF impacts air-sea heat exchange, inter-ocean heat distribution, and regional and global climate systems. However, during boreal winter, monsoon-driven buoyant South China Sea waters inhibit surface ITF flow and reduce heat transport to the Indian Ocean. Records of past monsoon influences on surface water variability in the Indonesian Seas are therefore critical to better understand the interactions between monsoon-driven ocean circulation and Indo-Pacific climate. In this talk, I present multi-century, coral-derived records of sea surface salinity and ocean circulation to examine the role of the East Asian Winter Monsoon (EAWM) in surface water mixing variability throughout the Makassar and Lombok Straits, located along main ITF pathways. This multi-site study documents that changes in the strength and state of the EAWM alter surface water circulation throughout the western Indonesian Seas, likely interacting with southward ITF transport and thus regional and global climate systems across the Indo-Pacific.