An extensive suite of conductivity-temperature-depth stations was obtained from the Baruna Jaya I during the southeast monsoon of 1993 and northwest monsoon of 1994, as part of the Indonesian/U.S. Arlindo project. The main objective of these cruises was to determine sources, pathways, and mixing histories of the throughflow water masses for the monsoon extremes. Water mass analysis indicates that the most penetrating route followed by Pacific water occurs within the Makassar Strait. This supports the notion that this strait carries the bulk of the Pacific to Indian throughflow, consisting of North Pacific Subtropical Water (upper thermocline Smax) and North Pacific Intermediate Water (lower thermocline Smin). The more attenuated Smax core during the northwest monsoon relative to the southeast monsoon suggests that the throughflow may slacken in that season. There is only minor contribution within the possible throughflow pathway east of Sulawesi. However, relative salty water of South Pacific origin is observed in the lower thermocline within the Seram and southern Maluku Seas, particularly in the northwest monsoon. Density-driven, sill depth overflow into the deep Banda Sea basin via the Lifamatola Passage also contributes to the total throughflow, though this contribution is likely to be minor. While some of the throughflow has been shown to pass through the Lombok Strait, water mass analysis clearly shows the Makassar throughflow turning into the Flores Sea and Banda Sea before curling southward into the Timor Sea and Indian Ocean.