Abstract. The short-term dynamics of carbon and water fluxes across the soil–plant–atmosphere continuum are still not fully understood. One important constraint is the lack of methodologies that enable simultaneous measurements of soil CO2 concentration and respective isotopic composition at a high temporal resolution for longer periods of time. δ13C of soil CO2 can be used to derive information on the origin and physiological history of carbon, and δ18O in soil CO2 aids in inferring the interaction between CO2 and soil water. We established a real-time method for measuring soil CO2 concentration, δ13C and δ18O values across a soil profile at higher temporal resolutions (0.05–0.1 Hz) using an off-axis integrated cavity output spectroscopy (OA-ICOS). We also developed a calibration method correcting for the sensitivity of the device against concentration-dependent shifts in δ13C and δ18O values under highly varying CO2 concentration. The deviations of measured data were modelled, and a mathematical correction model was developed and applied for correcting the shift. By coupling an OA-ICOS with hydrophobic but gas-permeable membranes placed at different depths in acidic and calcareous soils, we investigated the contribution of abiotic and biotic components to total soil CO2 release. We found that in the calcareous Gleysol, CO2 originating from carbonate dissolution contributed to the total soil CO2 concentration at detectable degrees, potentially due to CO2 evasion from groundwater. The 13C-CO2 of topsoil at the calcareous soil site was found reflect δ13C values of atmospheric CO2, and the δ13C of topsoil CO2 at the acidic soil site was representative of the biological respiratory processes. δ18O values of CO2 in both sites reflected the δ18O of soil water across most of the depth profile, except for the 80 cm depth at the calcareous site where a relative enrichment in 18O was observed.