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 its 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 to infer 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 up to 1 Hz using an Off-Axis Integrated Cavity Output Spectrometer (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 probably due to CO2 evasion from groundwater. Inward diffusion of atmospheric CO2 was found to be rather pronounced in the topsoil layers at both sites. No specific pattern was identified for δ18O in soil CO2 at the calcareous site, δ18O values reflected fairly well the δ18O of soil water at the acidic soil site.