Abstract Simple Ocean Data Assimilation (SODA) reanalysis data are used to produce a 50-yr record of flow through the Makassar Strait, the primary conduit for the Indonesian Throughflow (ITF). Two time series are constructed for comparison to the flow through the Makassar Strait as observed during 1997–98 and 2004–06: SODA along-channel speed within the Makassar Strait and Pacific to Indian Ocean interocean pressure difference calculated on isopycnal layers from SODA hydrology. These derived time series are compared to the total ITF as well as to the vertical distribution and frequency bands of ITF variability. The pressure difference method displays higher skill in replicating the observed Makassar ITF time series at periods longer than 9 months, particularly within the thermocline layer (50–200 m), the location of maximum flow. This is attributed to the connection between the thermocline layer and large-scale wind forcing, which affects the hydrology of the ITF inflow and outflow regions. In contrast, the surface layer (0–50 m) is more strongly correlated with local wind flow, and it is better predicted by SODA along-channel velocity. The pressure difference time series is extended over the 50-yr period of SODA and displays a strong correlation with ENSO as well as a correlation at the decadal scale with the island rule.