Using results from a high-resolution ocean general circulation model, this study identifies the impact of ocean dynamics on the mean seasonal cycle of sea surface temperature (SST) in the southeastern tropical Indian Ocean. An important question about the mechanisms of regional SST variation arises in a quick look at satellite-observed SST and ocean color. Although ocean color indicates a distinctive upwelling season from July to September, the SST depression off Java and Sumatra is small, forming a sharp contrast with other eastern boundary regions. The model results suggest an explanation of the process responsible for the small SST depression. Our analysis indicates that there are three dynamically different regimes within the region. First, near the coast of northwest Australia, surface heat flux controls the seasonal variation of SST, while horizontal advection and vertical entrainment are relatively weak. This result is consistent with previous studies. Second, south of Java and farther to the east, warm horizontal advection of the Indonesian throughflow (ITF) neutralizes the cold upwelling. The transport of the ITF, especially the outflow from the Lombok Strait, reaches its seasonal maximum in July–September, at the same time that the maximum upwelling occurs. Third, west of Sumatra, a thick barrier layer exists, which impedes the cold thermocline water from entering the mixed layer (ML). Although upwelling occurs, it has no significant effect on the SST as a result of the small vertical temperature gradient at the bottom of the ML.