We present a unique water column data set of dissolved inorganic carbon (DIC) and total alkalinity (TAlk) from a cruise to the western Indonesian Seas during the southeast monsoon, covering the Karimata Strait, western Java Sea, and Sunda Strait. Salinity‐normalized TAlk (NTAlk) in the surface water ranged 2,297–2,348 μmol kg⁻¹, very close to typical values observed in the tropical ocean. In the Karimata Strait, the Kapuas River plume was observed, featuring low salinity, DIC, and TAlk. In the western Java Sea, where waters were well mixed, we observed relatively homogeneous distributions of salinity, DIC, and TAlk. In the Sunda Strait, waters intruding from the Java Sea occupied the upper layer, and below was the Indian Ocean water with lower values of salinity, DIC, and TAlk. In its deep portion, depth profiles of normalized DIC and NTAlk were very similar to those observed in the Indian Ocean. Physical processes and air‐sea gas exchange exerted predominant controls on the carbonate system in the Karimata Strait and western Java Sea. While both processes play large roles in the Sunda Strait, a net DIC removal of 31 ± 23 μmol kg⁻¹ in the surface mixed layer were revealed. The drawdown of DIC is consistent with an overall supersaturation of dissolved oxygen (102–107%), suggesting significant organic carbon production. In the subsurface‐intermediate waters of the Sunda Strait mainly influenced by the advection of Indian Ocean water, a net DIC consumption of 54 ± 45 μmol kg⁻¹ was distinct, likely stimulated by the nutrients supplied from the Indian Ocean.

Research focusing on seagrass ecosystems as carbon storage has been conducted in various Indonesian waters. However, an essential aspect that remains unexplored is the simultaneous analysis of blue carbon storage in seagrass alongside carbon dioxide (CO₂) flux values, particularly within Karimunjawa waters. This study aims to assess the organic carbon stock and sea–air CO₂ flux in seagrass ecosystems in Karimunjawa. Our hypothesis posits that although seagrass ecosystems release CO₂ into the water, their role as blue carbon ecosystems enables them to absorb and accumulate organic carbon within seagrass biomass and sediments. This investigation took place in Karimunjawa waters, encompassing both vegetated (seagrass meadows) and unvegetated (non-seagrass meadows) areas during August 2019, 2020, and 2022. Over this period, the organic carbon stock in seagrass and sediment displayed an increase, rising from 28.90 to 35.70 gC_org m⁻² in 2019 and from 37.80 to 45.25 gC_org m⁻² in 2022. Notably, the expanse of seagrass meadows in Karimunjawa dwindled by 328.33 ha from 2019 to 2022, resulting in a total carbon stock reduction of the seagrass meadows of 452.39 tC to 218.78 tC. Sediment emerges as a pivotal element in the storage of blue carbon in seagrass, with sedimentary organic carbon outweighing seagrass biomass in storage capacity. The conditions in Karimunjawa, including a high A:B ratio, low dry bulk density, and elevated water content, foster a favorable environment for sediment carbon absorption and storage, facilitated by the waters’ CO₂ emission during the southeast monsoon season. Notably, our findings reveal that CO₂ release within vegetated areas is lower compared to unvegetated areas. This outcome underscores how seagrass ecosystems can mitigate CO₂ release through their adeptness at storing organic carbon within biomass and sediment. However, the presence of inorganic carbon in the form of calcium carbonate introduces a nuanced dynamic. This external source, stemming from allochthonous origins like mangroves, brown algae like Padina pavonica, and calcareous epiphytes, leads to an increase in sedimentary organic carbon stock of 53.2 ± 6.82 gC_org m⁻². Moreover, it triggers the release of CO₂ into the atmosphere, quantified at 83.4 ± 18.26 mmol CO₂ m⁻² d⁻¹.

The Indonesian seas are a renowned global biodiversity hotspot, yet nutrient sources and fluxes (especially the vertical flux) sustaining this richness remain unclear. Here, we used non‐atmospheric helium‐3 (³He) to constrain the vertical diffusion coefficient (K_d) in the Indonesian seas, which ranges from 5.2 × 10⁻⁵ to 2.3 × 10⁻³ m² s⁻¹ and averages 6.6 × 10⁻⁴ m² s⁻¹, a value notably higher than those found in the open ocean and in most marginal seas. We estimated that 6.9 ± 7.9 mmol m⁻² d⁻¹ of nitrate (NO₃⁻) is vertically transported into the surface mixed layer, that is, >90% of the total NO₃⁻ required to support a net community production (NCP) of 470 ± 467 mg‐C m⁻² d⁻¹. Regions with narrow straits, steep topography and dynamic circulation with strong vertical mixing display high NCP and chlorophyll‐a, suggesting that vertical nutrient transport dominates biological productivity. Findings highlight the importance of vertical mixing in supplying nutrients and maintaining the extraordinary biological productivity and diversity in the Indonesian seas.

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.