Jakarta Bay, a highly urbanized tropical estuary, exhibits methane ( \({\text{CH}}_{4}\) ) dynamics shaped by the interplay of terrestrial organic inputs, sediment redox stratification, and local hydrographic factors such as water depth, oxygen levels, and circulation. This study presents one of the first vertical assessments of sedimentary \({\text{CH}}_{4}\) distribution (0–100 cm below the seafloor) using a modified headspace technique and nondispersive infrared gas analysis. Field measurements conducted during two seasonal hydrographic conditions, the dry season (August 2023) and wet season transition (October 2023), revealed pronounced spatial and vertical variability in \({\text{CH}}_{4}\) accumulation. Nearshore and eastern stations showed elevated organic matter (OM) and bottom-water hypoxia and supported shallow sulfate–methane transition zones (SMTZs) at 30–40 cm depth and \({\text{CH}}_{4}\) concentrations reaching up to 1.2 µmol L−1. Conversely, offshore western stations exhibited deeper sulfate penetration (> 100 cm) and minimal \({\text{CH}}_{4}\) buildup (< 0.3 µmol L−1), reflecting more oxic and ventilated sediments. \({\text{CH}}_{4}\) flux across the sediment–water interface calculated using Fick’s first law ranged from slightly negative to positive but remained low in magnitude. These bidirectional fluxes suggest subtle gradients and localized redox control, with some stations exhibiting net \({\text{CH}}_{4}\) oxidation due to anaerobic oxidation of methane (AOM). Findings align with patterns in other eutrophic systems such as Chesapeake Bay and Bohai Sea, where eutrophication-driven stratification modulates methane cycling. The study underscores the need to integrate vertical profiling in methane research and highlights the importance of combining microbial analysis, OM characterization, and direct atmospheric flux measurements to refine emission estimates.
