An extensive suite of conductivity-temperature-depth stations was obta
ined from the Baruna Jaya I during the southeast monsoon of 1993 and n
orthwest monsoon of 1994, as part of the Indonesian/U.S. Arlindo proje
ct. The main objective of these cruises was to determine sources, path
ways, and mixing histories of the throughflow water masses for the mon
soon extremes. Water mass analysis indicates that the most penetrating
route followed by Pacific water occurs within the Makassar Strait. Th
is supports the notion that this strait carries the bulk of the Pacifi
c to Indian throughflow, consisting of North Pacific Subtropical Water
(upper thermocline S-max) and North Pacific Intermediate Water (lower
thermocline S-min). The more attenuated S-max core during the northwe
st monsoon relative to the southeast monsoon suggests that the through
flow may slacken in that season. There is only minor contribution with
in the possible throughflow pathway east of Sulawesi. However, relativ
e salty water of South Pacific origin is observed in the lower thermoc
line within the Seram and southern Maluku Seas, particularly in the no
rthwest monsoon. Density-driven, sill depth overflow into the deep Ban
da Sea basin via the Lifamatola Passage also contributes to the total
throughflow, though this contribution is likely to be minor. While som
e of the throughflow has been shown to pass through the Lombok Strait,
water mass analysis clearly shows the Makassar throughflow turning in
to the Flores Sea and Banda Sea before curling southward into the Time
r Sea and Indian Ocean.