Within the coastal zone, salt marshes often behave as atmospheric CO2 sinks, allowing for blue carbon (C) sequestration associated with intense autotrophic metabolism. However, C dynamics over salt marshes are complex since various biogeochemical processes and fluxes occur at different terrestrial–aquatic–atmospheric exchange interfaces and spatiotemporal scales. This study focuses on seasonal, tidal and diurnal variations of water pCO2, estimated water–air CO2 fluxes and controlling factors along two temperate shelf–estuary–marsh continuums. The latter include typical coastal systems with artificial salt marshes that have contrasting water management practices and primary producer types. Our high-frequency biogeochemical measurements (seasonal 24-hour cycles) highlighted a strong control of ecosystem typology on inorganic C dynamics with lower water pCO2 values in the artificial salt marshes, due to stronger biological activity and longer water residence times, than in the tidal estuary. In the marine-dominated estuary, water pCO2 variations (267 - 569 ppmv) were strongly controlled by tidal effects and phytoplankton activity particularly in spring/summer. On the contrary, the greatest amplitudes in water pCO2 were recorded in the artificial salt marshes (6 - 721 ppmv) due to intense macrophyte activity. In the rewilded marsh, eutrophication favoured spring/summer fast-growing macroalgae produced, in turn, strong fall atmospheric CO2 outgassing from degraded algae waters and thus a net annual source of CO2 to the atmosphere (17.5 g C m−2 yr−1). Conversely, specific management practices at the working marsh for salt-farming activity favoured rather slow-growing macrophytes (i.e. seagrasses) which greatly contribute to the yearly observed atmospheric CO2 sink (-97.7 g C m−2 yr−1). In this work, we suggest that salt marsh management can be used to control the contribution of primary producers to marsh C budget as atmospheric CO2 (sink and/or source).