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 autumn (September–October) 2024 using cavity ring-down spectroscopy combined with a water equilibration system. We explored how GHG levels relate to bay physical characteristics (i.e. topographic openness, sediment properties vegetation cover) and seawater properties (temperature, salinity, dissolved-oxygen saturation, chlorophyll-a, organic carbon, and nutrient concentrations), revealing significant seasonal variation of 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 autumn and N₂O higher in spring. CH₄ concentrations below 250 nmol L⁻¹ were negatively correlated with N₂O, while higher CH₄ levels showed a positive correlation, suggesting differences in the dominant sedimentary microbial pathways. Most bays acted as net GHG sinks in April and sources in September, with only one bay showing net source behaviour in both seasons. One bay that is subject to substantial human impacts (e.g. dredging, high nutrient loading, reduced vegetation cover) showed CO₂-equivalent CH₄ emissions that surpassed CO₂ uptake in this particular bay. CO₂-equivalent fluxes ranged from −195.2 to 793.6 mg CO₂ eq. m⁻² d⁻¹ (median: 131.5 mg CO₂ eq. m⁻² d⁻¹). This study is distinctive in simultaneously measuring all three major GHGs across multiple bays in relation to diverse environmental controls, offering a uniquely integrated understanding of coastal GHG dynamics. 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.