Abstract Strong El Ni?o and positive Indian Ocean Dipole (pIOD) events in 2015/2016 followed by relatively strong negative Indian Ocean Dipole (nIOD) and weak La Ni?a in 2016 events have affected hydrography conditions in the Indonesian Throughflow (ITF) region. Two research cruises were conducted using RV Baruna Jaya VIII in August and November 2016. These cruises aim to evaluate possible impact of those two climate mode events on the water mass characteristic in the outflow region of the ITF. Hydrographic data from those two cruises were combined with the sea surface temperature (SST) from the Advanced Very High Resolution Radiometer (AVHRR) and surface wind data from the European Centre for Medium-Range Weather Forecasts (ECMWF). The results showed that in the 2016 anomaly year, the cooler sea surface temperature was observed during the negative IOD (nIOD) event while the warmer temperature was found in the post of nIOD event. The observed water mass characteristics in the outflow region of the ITF revealed that the upper layer was dominated by the Indian Ocean water mass, while the Pacific Ocean water mass was observed in the deeper layer. The observed current data across the Sumba Strait showed that the South Java Coastal Current (SJCC) was observed in the upper layer, propagating eastward toward the Savu Sea. A few days later, the observed currents in the upper layer of the Ombai Strait revealed the ITF flow towards the Indian Ocean. Meanwhile, the lower layer showed an eastward flow towards the Ombai Strait.