Mapping of carbon dioxide and methane sea-air fluxes in coastal, shallow waters of the Stockholm archipelago, Baltic Sea

Shallow coastal waters play a crucial role in the global carbon cycle through the sea-air exchange of greenhouse gases such as carbon dioxide (CO₂) and methane (CH₄). These regions are hotspots for both sequestration and emission of these gases; however, their contributions to global and regional budgets remain poorly quantified. Understanding the spatial and temporal variability of CO₂ and CH₄ exchange in coastal waters is essential for refining our knowledge of the climate system, especially as these systems face increasing anthropogenic pressures that may significantly alter their gas dynamics. Here, we present findings on CO₂ and CH₄ fluxes from seven shallow (<6 m) sampling locations in the Stockholm archipelago, Baltic Sea. These locations represent four distinct habitat groups – macroalgae on pebbles/bedrock, sand, macrophyte communities, and reed beds – and were monitored across a full annual cycle using the floating chamber method. In the summer months, most habitats acted as CO₂ sinks, with the highest uptake recorded in the pebbles/bedrock habitat in July (-937 ± 161 mg m^-2 d^-1). During autumn and winter, however, all habitats shifted to CO₂ emission, peaking in the reed beds in October with an efflux of 1757 ± 328 mg m^-2 d^-1. Annually, five of the seven locations exhibited net CO₂ emissions. Further, all habitats were year-round sources of CH₄, with average monthly diffusive emissions ranging from 0.1 ± 0.01 mg m^-2 d^-1 to 26 ± 1.5 mg m^-2 d^-1. The fluxes generally followed a seasonal pattern, with higher emissions in summer and lower emissions in winter. Ebullition fluxes were observed in all habitats except the pebbles/bedrock, with monthly fluxes reaching up to 249 mg m^-2 d^-1 and contributing between 20 and 98% of the total annual CH₄ flux in the locations where it occurred. Upscaling the CO₂ and CH₄ fluxes over waters < 6 m in the Stockholm archipelago (680 km²) rendered CO₂-equivalent fluxes for a 100-year timescale ranging between -0.04 and 0.3 Tg CO₂-eq yr^-1, where 80% of the uncertainty from flux variability could be attributed to CH₄. These findings suggest that CH₄ plays a much larger role in the sea-air exchange of carbon-based greenhouse gases than previously estimated in northern, temperate coastal waters.