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The Land–Ocean Aquatic Continuum (LOAC) is a critical and complex component of the global carbon cycle, regulating the transfer, transformation, and evasion of carbon from terrestrial ecosystems to the coastal ocean. Last layer of this continuum before the coastal ocean, estuaries play a dual role: 1) as reactors that process organic and inorganic carbon and 2) as sometimes significant sources of CO₂ emissions to the atmosphere compared to their modest surface areas. These processes are tightly controlled by a wide array of external factors including upstream land-based emissions (influenced by lithological context, land use, etc.), riverine transport and in-stream biogeochemical transformations, as well as internal estuarine morphology, hydrodynamics and metabolism. With over 50 000 estuaries worldwide and a wide heterogeneity between systems, performing an exhaustive carbon budget analysis, even regionally is a major but necessary challenge to better constrain the carbon land-ocean exchange and the contribution of estuaries to CO2 budgets.To investigate the coupling between lateral carbon fluxes and atmospheric CO₂ exchanges over a continuous stretch of coast, batch simulations of the 1D depth integrated generic estuarine hydrological/biogeochemistry C-GEM has emerged as a suitable solution because of its design build on limited data and computing demand. In an application on the Atlantic French coast, estuarine dynamics were explicitly represented in time and space for 35 selected macro-tidal estuaries. This regional application quantifies the cascading fluxes of Organic Carbon (OC), Dissolved Inorganic Carbon (DIC), from the upstream influence of tides to the estuarine outlets, while simulating air–water CO₂ exchanges within estuaries. This exercise is based on a structured database that compile an exhaustive inventory of all aquatic measurements at the upstream boundary of the estuarine modelling domain (for all watersheds larger than 300 km²), as well as along the estuarine longitudinal profiles themselves for model validation.Our integrated approach allows the establishment of a consistent regional carbon budgets that account for terrestrial inputs and estuarine processing, coastal exports, and CO₂ evasion to the atmosphere. Our simulations indicate that estuaries along the French Atlantic coast act predominantly as net sources of CO₂, with strong spatial variability driven by size, watershed characteristics, riverine carbon loads, and estuarine residence times. The fraction of riverine carbon loads that is outgassed towards the atmosphere as CO2 within the estuary ranges from a few percents to 20% from the smaller systems to the largest. By detailing the nature and intensity of carbon fluxes in the LOAC estuarine compartment, this work highlights the importance of proposing integrated land-sea modelling approaches that explicitly include estuarine interfaces in order to constrain regional carbon budgets and national and continental greenhouse gas inventories. Moreover, it opens to door to longer time scale simulations to disentangle the natural component of the global estuarine carbon budget from its anthropic perturbation, partitioning that is currently virtually unknown.