Soil CO2 and N2O concentrations were simulated with a model predicting C and N transport in the vadose zone during a 7-mo field experiment, after maize (Zea mays L.) harvesting and incorporation of maize residues into the soil. The gas transport model was based on the dusty gas theory and combined with the PASTIS model. During the experiment, soil atmosphere (CO2 and N2O), soil solution (NO3− and dissolved organic carbon [DOC]), soil water content and temperature, and potential denitrifying and aerobic respiratory activities were measured in a 2.50-m-thick soil profile. Soil gas concentrations were correctly simulated even though the model did not simulate all the biological processes that produced N2O. Nitrous oxide concentration peaks after rain were slightly overestimated, as the WFPS (water-filled pore space) was not estimated accurately enough to predict local anoxic conditions. To model CO2 concentrations, account had to be taken of DOC adsorption onto soil mineral particles and of zymogenous biomass death during the period when the ground was frozen. The model satisfactorily simulated NO3− concentrations in the top soil profile, notably during major rainfall events, and maize residue dry matter loss during the experiment. The modeling of biological processes needs to be improved to provide a better simulation of C and N transport in the vadose zone. In particular, the use of WFPS was not sufficient to predict anoxic periods; simulations should improve if soil aggregate structure is also taken into account.