Rates of soil respiration (CO2 effluxes), subsurface pore gas CO2/O2 concentrations, soil temperature and soil water content were measured for 15 months in two temperate and contrasting Danish forest ecosystems: beech (Fagus sylvatica L.) and Norway spruce (Picea abies [L.] Karst.). Soil CO2 effluxes showed a distinct seasonal trend in the range of 0.48–3.3 μmol CO2 m−2 s−1 for beech and 0.50–2.92 μmol CO2 m−2 s−1 for spruce and were well-correlated with near-surface soil temperatures. The soil organic C-stock (upper 1 m including the O-horizon) was higher in the spruce stand (184±23 Mg C ha−1) compared to the beech stand (93±19 Mg C ha−1) and resulted in a faster turnover time as calculated by mass/flux in soil beneath the beech stand (28 years) compared to spruce stand (60 years). Observed soil CO2 concentrations and effluxes were simulated using a Fickian diffusion-reaction model based on vertical CO2 production rates and soil diffusivity. Temporal trends were simulated on the basis of observed trends in the distribution of soil water, temperature, and live roots as well as temperature and water content sensitivity functions. These functions were established based on controlled laboratory incubation experiments. The model was successfully validated against observed soil CO2 effluxes and concentrations and revealed that temporal trends generally could be linked to variations in subsurface CO2 production rates and diffusion over time and with depths. However, periods with exceptionally high CO2 effluxes (> 20 μmol CO2 m−2 s−1) were noted in March 2000 in relation to drying after heavy rain and after the removal of snow from collars. Both cases were considered non-steady state and could not be simulated.