Peatlands store organic carbon available for decomposition and transfer to neighboring water bodies, which can ultimately generate carbon dioxide (CO₂) emissions. The objective of this study was to clarify the biogeochemical functioning of open‐water peatland pools and their influence on carbon budgets at the ecosystem and global scale. Continuously operated automated equipment and monthly manual measurements were used to describe the CO₂ and CH₄ dynamics in boreal ombrotrophic peatland pools and porewater (Québec, Canada) over the growing seasons 2019 and 2020. The peat porewater stable carbon isotope ratios (δ¹³C) for both CO₂ (median δ¹³C‐CO₂ : −3.8‰) and CH₄ (median δ¹³C‐CH₄ : −64.30‰) suggested that hydrogenotrophic methanogenesis was the predominant degradation pathway in peat. Open‐water pools were supersaturated in CO₂ and CH₄ and received most of these dissolved carbon greenhouse gases (C‐GHG) from peat porewater input. Throughout the growing season, higher CO₂ concentrations and fluxes in pools were measured when the water table was low—suggesting a steady release of CO₂ from deep peat porewater. Higher CH₄ ebullition and diffusion occurred in August when bottom water and peat temperatures were the highest. While this study demonstrates that peatland pools are chimneys of CO₂ and CH₄ stored in peat, it also shows that the C‐GHG concentrations and flux rates in peat pools are comparable to other aquatic systems of the same size. Although peatlands are often considered uniform entities, our study highlights their biogeochemical heterogeneity, which, if considered, substantially influences their net carbon balance with the atmosphere.