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The present work deals with modeling of the fate of nitrogen through a vertical flow constructed wetland (VFCW) using gravel, treating directly domestic raw wastewater. The experimental design of the work involved lab-scale and full-scale experiments to calibrate the multi-component reactive transport model for constructed wetlands (CW2D). Besides measured values for the hydraulic parameters and the maximum autotrophic growth rate, we calibrated two other parameters (oxygen re-aeration rate and adsorption coefficients of ammonium) to reduce the difference between predictions and measurements. The obtained model determined the time-variation of nitrogen concentrations in the effluent with reasonable performances. With the use of the modelwedemonstrate that, during feeding period, the ammonium was significantly adsorbed onto organic matter besides conversion into nitrates; the adsorbed mass of ammonium was nitrified during the rest period provoking high nitrates concentrations during the first two subsequent batches. We also demonstrated that heterotrophic biomass was mainly present in the sludge layer (first 20 cm), whereas autotrophic biomass was located in the first 50cm of the VFCW (sludge and 30cm biomat).