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Coastal shallow ecosystems vary widely in physical conditions, habitat structure, and biodiversity, resulting in differences in biogeochemical processes and greenhouse gas (GHG) emissions. Benthic and pelagic processes, together with their interactions, regulate the production and consumption of carbon dioxide (CO2) and methane (CH4) across coastal ecosystems, potentially giving rise to intense, localized episodes of production or emission known as “hot moments” at specific sites, or “hot spots”. However, despite their importance for regional and global carbon cycles, these processes remain poorly characterized in many coastal environments due to their strong spatial and temporal heterogeneity.We measured surface and bottom seawater biogeochemical properties using a state-of-the-art flow-through system equipped with a cavity ring-down system Picarro G2201-i, to measure CO2 and CH4 concentrations and stable carbon isotope composition, coupled with sensors for physical (temperature and salinity) and biogeochemical (chlorophyll-a (Chl-a), turbidity, colored dissolved organic matter (cDOM), dissolved oxygen (DO)) parameters. Sampling took place from June 2024 to May 2025, with 21 sites sampled in SW Finland, covering diverse soft-sediment habitats from sheltered to exposed areas along a salinity gradient.Surface water partial pressure of CO2 (pCO2) and CH4 concentration ranged from 73.61 µatm to 3078.49 µatm, and from 4.48 nmol/L to 1104.77 nmol/L, respectively, with lower values observed for both parameters during spring, while higher values were observed during the summer months. Bottom water pCO2 ranged 89.09 µatm to 1969.67 µatm and the CH4 ranged from 4.68 nmol/L to 5145.44 nmol/L. For bottom waters, both minima appeared in spring, while the maxima appeared in summer months for the pCO2 and during autumn for CH4.The lowest surface pCO2 values were associated with elevated Chl-a concentrations (57.94 µg/L), indicating a relation between low pCO2 and periods of high phytoplankton biomass and enhanced autotrophic activity. This pattern was observed during the spring bloom and persisted to a lesser extent during the summer, when Chl-a concentrations remained relatively high. In contrast, surface pCO2 and CH4 concentrations increased later in the season, with elevated values during summer and maxima generally occurring in autumn. This seasonal increase coincided with declining surface DO concentrations (minimum 215.92 µM) and increasing cDOM concentrations (up to 26.02 µg/L), reflecting pronounced seasonal changes in biogeochemical conditions.In addition to seasonal variability, there was strong spatial heterogeneity across sites with different exposures. Sheltered locations consistently showed higher and more variable concentrations of pCO2 and CH4, especially during summer and autumn. In contrast, exposed sites had lower GHG levels and less seasonal fluctuation, while semi-exposed sites generally showed intermediate values. These spatial patterns were visible in both surface and bottom waters, with the largest contrasts observed in bottom-water CH4 concentrations, suggesting a key role of seafloor habitats.All in all, these findings demonstrate that seasonal ecosystem changes significantly influence coastal GHG variability, highlighting the role of spatial-temporal heterogeneity as a key factor for improving the understanding of coastal GHG dynamics.