In this study, partial nitrification coupled with denitrification is modeled in a hybrid biofilm reactor with different hydraulic saturation conditions. The activated sludge model with two-step nitrification is implemented in GPS-X software. Hydrodynamic modeling by retention time distribution analysis and biokinetic measurement by respirometric tests are two significant parts of model calibration. By combining these two parts, partial nitrification in the aerobic part of the column is well simulated with a good agreement between experimental and modeled effluent concentrations of NH4 (+) and NO2 (-). Particularly, fully hydraulic saturation condition contributes to the large hydraulic volume of 1.9 L and high produced NO2 (-) concentration around 40 mg L(-1). However, modeling denitrification still needs to be improved with more calibrated parameters. Furthermore, three alternatives are proposed for the optimization of reactor design and operation.