Intraseasonal variability [ISV] in the Makassar Strait thermocline is examined through the analysis of along-channel flow, regional sea level anomaly and wind fields from January 2004 through November 2006. The dominant variability of 45–90 day in the Makassar Strait along-channel flow is horizontally and vertically coherent and exhibits vertical energy propagation. The majority of the Makassar ISV is uncoupled to the energy exerted by the local atmospheric ISV: instead the Makassar ISV is due to the combination of a remotely forced baroclinic wave radiating from Lombok Strait and deep reaching ISV originating in the Sulawesi Sea. Thermocline depth changes associated with ENSO influence the ISV characteristics in the Makassar Strait lower thermocline, with intensified ISV during El Niño when the thermocline shallows and weakened ISV during La Niña.