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. Using floating chambers, this study quantified seasonal and annual CO2 and CH4 fluxes in common Baltic Sea habitats, 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 3512 ± 704 mg CO2 m−2 d−1, with macroalgae and reed habitats exhibiting distinct flux ranges. Apart from macroalgae, all habitats exhibited a net annual CO2 efflux. Diffusive CH4 fluxes varied seasonally, from 0.1 ± 0.01 to 26 ± 1.5 mg CH4 m−2 d−1, with peak emissions in summer. Ebullition occurred from March to October, reaching up to 232 mg CH4 m−2 d−1 and contributed substantially to annual carbon-based greenhouse gas fluxes in the sand, mixed-substrate, and reed habitats. Contrary to previous findings that ebullition is confined to muddy, organic-rich sediments, this study found the highest CH4 ebullition in vegetated sand habitats, indicating a broader spatial extent of intense CH4 release than previously assumed. Upscaling to the shallow-water (< 6 m) zone of the Stockholm archipelago yielded total CO2-equivalent fluxes of between −0.01 and 0.2 Tg CO2eq yr−1 (100-year timescale). For comparison, Stockholm’s energy- and transport sectors emit ∼ 1.2 Tg CO2-eq yr−1, suggesting the shallow coastal zone could be a small, but non-negligible regional source for carbon-based greenhouse gases.