Within the coastal zone, salt marshes are often considered as atmospheric CO2 sinks associated to a significant autotrophic metabolism and sediment carbon (C) storage. However, C dynamics over salt marshes are complex since various processes and fluxes take place at the different terrestrial-aquatic-atmospheric exchange interfaces and spatio-temporal scales. This study focuses on diurnal, tidal and seasonal variations of subsurface water partial pressures of CO2 (pCO2), estimated water-atmosphere CO2 fluxes and associated controlling factors measured along a temperate tidal bay – channel – salt marsh continuum of the French Atlantic coast. High-frequency biogeochemical measurements performed over 24-hour cycles at four contrasted stations highlighted a strong biological control on pCO2 at the diurnal scale. Indeed, at dyked salt marsh stations, daytime macroalgae and phytoplankton photosynthesis produced large water CO2 undersaturation periods (72 ± 36 % per 24 hours) that resulted in a mean annual atmospheric CO2 sinks of -0.11 ± 0.38 mmol m2 h-1 characterized by strong diurnal and seasonal variations. In contrast, at more turbid channel water stations, lower primary production activity associated with microbial type network induced larger oversaturation and an overall CO2 source to the atmosphere ranging between -0.07 and 1.43 mmol m2 h-1 over the year. Other non-temperature effect such as tidal advection and management practices complicated even more pCO2 and atmospheric flux dynamics highlighting the need for further integrative measurements over these systems.