The transfer of Pacific water into the Indian Ocean through the Indonesian seas affects the heat and freshwater budgets of both oceans. The observed transport in the Makassar Strait, the primary Indonesian throughflow pathway, from January 2004 through November 2006 is 11.6 ± 3.3 Sv (Sv = 106 m3/s). This transport is 27% larger than observed during 1997 when a strong El Niño suppressed the flow. The 2004-06 Makassar transport displays clear seasonal behavior, with associated heat and freshwater variability, in contrast to the El Niño dominated 1997 transport. The 2004-06 transport reached maximum values towards the end of the northwest and southeast monsoons, with minimum transport are in October-December. A sustained high transport is observed in early 2006, perhaps in response to an La Niña condition. The maximum throughflow occurs within the thermocline, as in 1997, though the longer 2004-06 measurements also reveal a shallowing of transport as speeds increase. The transport-weighted temperature is 15.6°C in 2004-06, nearly 1°C warmer than that observed in 1997, presumably a consequence of El Niño.