The isothermal layer, mixed layer, and barrier layer in the southeastern tropical Indian Ocean are investigated using historical hydrographic and recent Argo-float profile data. The annual average isothermal and mixed layers are deep (>50 m) near the equator, but they do not have the same topographic structure. The mixed layer is more orientated along the coastline owing to the effect of precipitation and runoff. This forms a thick barrier layer (>25 m) to the west of Sumatra. The thickness decreases to 10 m near eastern Java and less farther to the east and south. The seasonal variation of barrier layer along the equator and off Sumatra/Java is a consequence of interplay between annual and semiannual variations. Surface water convergence, wave propagation, and precipitation are essentially responsible for these variations. Annual (1 cpy) variation is dominant in most of the region studied except for two locations where semiannual variation is also large. The semiannual variation in isothermal depth (ID), mixed layer depth (MLD), and barrier layer thickness (BLT) is most evident along the equator, with a comparable strength to the annual variation. The other region of large semiannual variation in ID and MLD is off Northwest Australia, but no significant variation in BLT is observed there.