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Variations of volume transport in the Halmahera Sea are strongly influenced by the El Nino Southern Oscillation (ENSO). Based on the ENSO Index at Nino 3.4, in 2011 La Nina event took place with a strength of -1.4, while in 2015 El Nino occurred with a strength of +2.6. This paper discusses the variation of transport volume caused by the ENSO phenomenon based on the results of the Regional Ocean Model System (ROMS). On the Halmahera Sea at a latitude of 0.3(^circ)S with a width of 67 km and a depth of up to 300 m, net volume transport always moves southward. The largest volume transport in La Nina 2011 occurred in September-October, which was -8.9 Sv. Meanwhile, in El Nino 2015 the largest volume transport occurred in July-August, which was equal to -4.9 Sv. The cross correlation coefficient between volume transport and SOI in 2011 and 2015 respectively was r = 0.55 and r = 0.61, where these results indicate a strong relationship.