Few studies have examined CO2 sources and pathways along the soil–aquifer–stream–atmosphere continuum. We measured the water concentration of dissolved CO2, HCO3–, and dissolved organic carbon (DOC), together with ancillary variables (pH, total alkalinity [TA], and major ions [Ca2+, Mg2+, SO42-, NO3–]), in piezometer transects and adjacent streams at a monthly interval over a 5-year period (2019–2023). Such a continuum was studied within a small catchment underlain by carbonate geology and subject to intensive agriculture.On the basis of the values of Ca2+, Mg2+, SO42-, and alkalinity in the upslope and downslope piezometers, we assumed that the more mineralized downslope water would characterize the slow groundwater flow component of the stream, while the less mineralized upslope water would reflect a fast sub-surface flow (surface runoff + agricultural drainage flow). These water flows components were calculated using the HYPE calibrated hydrological model.Accounting for weathering reactions and using a mass balance of dissolved C fluxes, we found that the total alkalinity flux (as HCO3–) reaching the river (amounting to 29 Mmol yr−1, i.e., 79 kgC ha−1 yr−1) derived for about one third from soil CO2 respiration, one third from carbonate dissolution induced by the reaction with CO2, and one third from carbonate dissolution induced by the acidity generated by nitrification of reduced N fertilizers.The groundwater CO2 fluxes to the stream (13 Mmol y-1, i.e., 36 kgC ha−1 yr−1) were 2 orders of magnitude lower than the total direct soil CO2 flux emitted to the atmosphere. Most (at least 95 %).of the groundwater CO2 fluxes was degassed once reaching the stream.Dissolved organic carbon flux to the stream represented only ∼ 2 % of the total dissolved carbon flux to the stream; the input of dissolved CO2 in rainfall to the soil–aquifer system amounted to less than 1 % of this total dissolved carbon flux to the stream.The carbonate weathering induced by soil respired CO2 amounted to ∼ 26 kgC ha−1 yr−1 in the Avenelles sub-catchment, representing ∼ 0.5 ‰ yr−1 of the total soil organic carbon stock. The alkalinity flux generated by this process might hence act as significant soil transient CO2 sink, depending on the prevalence of downstream processes affecting the stream carbonate buffering and speciation.