AbstractThe regional INDESO model configured in the Indonesian seas from 2008 to 2016 is used to study the mechanisms responsible for the variability of the currents in the Sulawesi Sea of the Indonesian seas. The model simulation compares reasonably with the seasonal to interannual variability of the moored current meter observations in the upper 350 m or so of the Maluku Channel during 2015 and 2016. The interannual variability of the currents in the eastern Sulawesi Sea in the model is found to be associated with both the Pacific and Indian Ocean remote forcing. Lag correlation analysis and a theoretical linear wave model simulation suggest that both the equatorial Kelvin waves from the Indian Ocean and the coastally trapped Kelvin waves from the western Pacific along the Philippine coast can propagate through the Indonesian seas and arrive at the Maluku Channel. In particular, from mid‐2015 to 2016 the Indian Ocean Kelvin waves are found to significantly impact the sea level anomaly variability in the Maluku Channel. The results indicate the importance of Indo‐Pacific planetary waves to the interannual variability of the currents in the Sulawesi Sea at the entrance of the Indonesian seas.