Coastal ecosystems are critical components of the global carbon cycle, exerting a disproportionate influence on the carbon budget despite their limited spatial extent. Estuaries remain understudied despite being dynamic sources of the three most potent greenhouse gases (GHGs): carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O). Such shallow coastal ecosystems are highly heterogeneous, shaped by strong physical, biogeochemical, and biological gradients. Combined with spatial variability in coastal biodiversity, these gradients strongly shape carbon cycling at both local and global scales. However, large uncertainties persist due to limited and spatially patchy measurements, highlighting the need for improved constraints on GHG budgets and their sensitivity to biodiversity loss and climate change.</p> <p>We measured surface seawater partial pressure of CO₂ (pCO₂), CH₄, and N₂O concentrations, along with seawater physical and biogeochemical properties, and air-sea gas exchange, at 21 sites in southwest Finland (Baltic Sea). Sampling followed a transition from estuarine inner bays to the outer archipelago, covering diverse soft-sediment habitats, from sheltered to exposed areas, across a salinity gradient. Surface water pCO₂ and N₂O concentration ranged from undersaturated (160 ppm and 9 nmol L^-1, respectively) to supersaturated (2521 ppm and 25 nmol L^-1, respectively), compared to the atmosphere, resulting in an uptake of -36 and -0.0021 mmol m^-2 d^-1, and a release up to 220 and 0.0383 mmol m^-2 d^-1, respectively. CH₄ concentrations were consistently supersaturated (19 to 469 nmol L^&ndash;1) compared to the atmosphere, resulting in a net source to the atmosphere from 0.014 to 1.39 mmol m^&ndash;2 d^&ndash;1.</p> <p>Freshwater input from the Karjaanjoki River and its mixing with seawater mainly determined the overall spatial patterns of GHGs. However, deviations from this salinity-driven control were observed. In sheltered sites within the archipelago, elevated pCO₂, CH₄, and N₂O concentrations likely reflected benthic processes, including enhanced organic matter respiration and methanogenesis in warm, late-summer shallow waters, where limited oxidation favoured CH₄ accumulation. At exposed sites, mixing processes had a stronger control, resulting in lower GHG concentrations. Our results show that both physical mixing and benthic processes influence coastal GHG dynamics, with benthic ecosystems playing a key but still poorly constrained role. Air&ndash;sea GHG exchanges were dominated by CO₂, while CH₄ and N₂O contributed differently as a source and a sink. The balance between production and consumption processes, particularly within benthic habitats, is therefore critical for understanding coastal contributions to the global carbon budget.