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A prominent ocean region exhibiting depleted oxygen concentration is the northern Indian Ocean, whose projected deoxygenation trend in response to climate change requires a comprehensive understanding of the roles of ocean dynamics. We present newly compiled in situ data across platforms (e.g. cruises, Argo, buoy) in the Indonesian coasts of Sumatra and Java between 2010–2022. Combined with reanalysis products, our data detect oxygen-depleted waters attributed to the eastward advection of the northern Indian Ocean waters and monsoon-driven coastal upwelling. Oxygen limited zones (OLZs, DO < 60 μmol kg-1) occupy various depths off the Sumatra-Java coasts, in which dissolved oxygen (DO) reaches ~40 μmol kg-1 in northwest Sumatra. The eastward propagating Equatorial Counter Current plays a major role in delivering the oxygen-depleted waters during the boreal summer; similarly, the South Equatorial Counter Current in the winter monsoon and the Wyrtki Jet during the transition months. Coastal upwelling regulates DO variations via primary production and the respiration of organic matter at intermediate depths in southern Java as the upwelled waters being advected westward towards Sumatra in the summer monsoon. Indonesian Throughflow with enriched organic matter modifies the oxygenated-depleted waters at its outlets. We observe a trend towards deepened OLZ in western Sumatra, while positive Indian Ocean Dipole events (2006, 2012, 2015, 2019) lower DO in the thermocline depths of southern Java on the interannual timescale. Altogether, high-resolution observational biogeochemical data are key to advance our understanding of dynamical DO changes in the southeastern tropical Indian Ocean under the global deoxygenation trend. [ABSTRACT FROM AUTHOR]