In order to better understand nitrogen species transport and transformation in the saturated zone, it is essential to predict the contaminant concentration in the unsaturated zone as the concentration profiles estimated from unsaturated zone forms as the input for estimation of contaminant concentration in the saturated zone. Since the nitrogen transformations occur in the presence of bacteria, there is a need to account the influence of biological clogging to develop comprehensive model of nitrogen species transport. In this study, a one-dimensional numerical model is developed to investigate the nitrogen species transport in an unsaturated porous media along with microbial clogging process. Results suggest that hydraulic conductivity is enhanced initially due to increase in the water content followed by a significant reduction at larger simulation time resulting from bioclogging. As bioclogging mitigates the hydraulic conductivity significantly, a considerable delay is observed in the ammonium nitrogen and nitrate nitrogen transport with reference to the system without bioclogging. In addition, the effect of oxygen mass transfer coefficient on biological clogging was evaluated. Numerical results suggest that as the oxygen mass transfer is decreased the ammonium nitrogen and nitrate nitrogen concentration travels a larger depth. Further numerical results strongly suggest that nitrogen species transport in the unsaturated zone is significantly affected by the presence of biological clogging. © 2014, Springer-Verlag Berlin Heidelberg.