A numerical model is developed to predict the nitrogen species concentration in an unsaturated subsurface system due to vertical leaching from wastewater and urea applied paddy field. The important processes like oxygen mass transfer from air phase to water phase and biological clogging due to microbial growth and their impact on nitrogen transformation are considered in this study. Results suggest that a rising and falling trend is observed for hydraulic conductivity in the presence of biological clogging, in which the rise is due to the influence of increase in water saturation and the fall is due to the increase in microbial saturation. The numerical results show that when the total nitrogen applied is 25mg/l continuously by wastewater application, the nitrate nitrogen concentration varies between 18 and 23mg/l at different depths in the absence of biological clogging and between 0 and 24mg/l in the presence of biological clogging. But in the case of 360kgNha-1 urea applied during the transplanting time (first day), the nitrate nitrogen concentration varies between 3 and 8mg/l at different depths in the absence of biological clogging and approximately 0mg/l throughout the depth of the soil column in the presence of clogging. The nitrate nitrogen concentration is 12 and 6mg/l at 100 and 200cm depth, respectively, for the case of three-time split fertilizer application in the presence of biological clogging. In both wastewater and fertilizer application cases, the biological clogging process induces unsaturated hydraulic conductivity reduction which helps to increase the contact time, accelerates nitrogen species transformations and eventually reduces the risk of nitrogen species contamination in groundwater. © 2014 Elsevier B.V.