Spatio-temporal variability of greenhouse gas concentrations and fluxes in shallow coastal bays of the western Baltic Sea

Abstract. Coastal ecosystems play a crucial role in greenhouse gas (GHG) dynamics but are less studied than open oceans or terrestrial systems. This study measured concentrations of carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) in six shallow bays of the wider Stockholm Archipelago during spring (April) and fall (September–October) 2024 using cavity ring-down spectroscopy combined with a water equilibration system. We explored how GHG levels relate to bay characteristics and seawater properties, revealing significant seasonal variation concentrations. Surface water pCO₂ ranged from 225–1372 ppm, CH₄ from 3.6–580 nmol L⁻¹, and N₂O from 8–20.8 nmol L⁻¹ with pCO₂ and CH₄ higher in fall and N₂O higher in spring. CH₄ concentrations below 250 nmol L⁻¹ negatively correlated with N₂O, while higher CH₄ levels showed a positive correlation, indicating a shift in biogeochemical processes. All bays except the two most open ones (which acted as net sinks in spring) served as GHG sources at the time of sampling, with one anthropogenically degraded bay showing CH₄ emissions that surpassed CO₂ uptake. CO₂-equivalent fluxes ranged from -76.1 to 710.8 mg CO_2-eq m⁻² d⁻² (median: 56.9 mg CO2-eq m⁻² d⁻²). These findings highlight the variability and complexity of coastal ecosystems and demonstrate the importance of high-resolution measurements for accurate up-scaling of fluxes from these dynamic environments.