Shallow coastal marine habitats are hotspots for carbon dioxide (CO₂) and methane (CH₄) exchange with the atmosphere, yet these fluxes remain poorly quantified, limiting their integration into global and regional carbon budgets. With the use of floating chambers, this study quantified seasonal and annual CO₂ and CH₄ fluxes in common Baltic Sea habitats using, including macroalgae-covered coarse sediments, sparsely to densely vegetated sands, submerged plant-covered mixed substrates, and reed-dominated muds. Monthly average CO₂ fluxes ranged from -937 ± 161 to 3 512 ± 704 mg m^-2 d^-1, with macroalgae and reed habitats exhibiting distinct flux ranges setting them apart from the sand and mixed substrate habitats. Apart from the macroalgae, all habitats exhibited a net efflux of CO₂ on an annual basis. Diffusive CH₄ fluxes varied seasonally, from 0.1 ± 0.01 to 26 ± 1.5 mg m^-2 d^-1 with peak emissions in summer. Ebullition fluxes occurred between March and October, reaching up to 232 mg m^-2 d^-1 and significantly contributed to, or even dominated, the annual exchange of both CO₂ and CH₄ in the sand, mixed substrate, and reed habitats. Upscaling these fluxes to the shallow-water (< 6 m) zone of the Stockholm archipelago yielded total CO₂-equivalent fluxes of between -0.01 and 0.2 Tg CO₂-eq yr^-1 on a 100-year timescale. In comparison, Stockholm’s energy- and transport sector emits approximately 1.2 Tg CO₂-eq yr^-1, suggesting that the shallow-water coastal zone could be a small, but significant contributor to the total source strength of the Stockholm region.