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NCEP reanalysis wind data from 1948 to 2016 and Makassar Strait transport from 2004 to 2011 are used to construct a multi-decadal timeseries of 0–300 m Makassar Throughflow using a back-propagation (BP) neural network. Based on the 2004–2015 Makassar timeseries, 0–300 m transport accounts for 75% (±8%) of the total Makassar throughflow. Results from the INSTANT program 2004–2006 indicate that the Makassar throughflow provides 78% of the Indonesian Throughflow (ITF) within the upper 1000 m (77% of the full depth ITF). As the ITF is driven largely by North Pacific winds, we use the North Pacific zonal wind to construct a 68-year timeseries of 0–300 m Makassar Throughflow to trace interannual to decadal variability. The constructed timeseries has a mean transport of 9.2 ± 1 Sv within the 0–300 m layer. Using the 2004–2015 statistics this converts to a total Makassar Strait throughflow of 12.2 Sv and using the 2004–2006 INSTANT data, to a total ITF within the upper kilometer of 14.7 Sv. The Makassar throughflow decreases from 1948 to 1995, increases after 1995, then rapidly decreases after 2013, which agrees with the Pacific to Indian inter-ocean pressure difference across the Indonesian seas based on SODA reanalysis with a correlation coefficients of 0.6. The Pacific Decadal Oscillation (PDO) and El Nino-Southern Oscillation (ENSO), have correlation coefficients with the constructed Makassar throughflow of −0.6 and −0.4 respectively. [ABSTRACT FROM AUTHOR]