Nitrate pollution in groundwater arising from wastewater and fertiliser application through vadose zone is a major problem and it causes a prime risk to groundwater-based drinking water supplies. In this study, a one-dimensional numerical model is developed to investigate the nitrogen species transport in unsaturated porous media along with mass transfer of oxygen from gaseous phase to aqueous phase. Further, the temperature-dependent nitrogen transformation rates, oxygen solubility in an aqueous phase from gaseous phase, and oxygen diffusion coefficient have been successfully incorporated. Results suggest that the temperature-dependent oxygen diffusion coefficient is significant in case of temperature variation between 30 and 45 °C, whereas the temperature-dependent oxygen solubility and transformation rate are found to be the critical parameters influencing the nitrogen species transport when the temperature variation is between 10 and 30°C. In the temperature range between 30 and 45°C, the model performance marginally improved compared with that of the same under isothermal condition. But in the case of variation between 10 and 30°C, the nitrate nitrogen concentration has higher variation during non-isothermal conditions when compared with isothermal conditions. Moreover, the results suggest that the dissolved oxygen concentration is also significantly affected by non-isothermal conditions. © 2013 Copyright Taylor and Francis Group, LLC.