The transport of nitrogen coming from wastewater applied agricultural field is a major problem in assessing the vulnerability of groundwater contamination. In this study, laboratory column experiments are conducted in order to simulate the paddy, groundnut and wheat irrigation with wastewater. The experiments are carried out with high clay content (≈35%) soil from Kancheepuram, Tamilnadu and low clay (≈9%) soil from Ludhiana, Punjab, India. Furthermore, a numerical model and HYDRUS-1D model are developed to simulate the experimental results. The experimental results show that there is no effluent collected at the bottom of the column during groundnut irrigation in Kancheepuram soil and effluent collected except during first irrigation in the case of wheat irrigation in Ludhiana soil. The experimental and numerical results illustrate that when 50 mg/l of ammonium and 20 mg/l of nitrate nitrogen applied during paddy irrigation, the peak nitrate nitrogen concentration of 50 mg/l is arrived after 10 days in Kancheepuram soil due to low permeability and relatively less background soil nitrogen. But in the case of Ludhiana soil with 94 mg/l of total nitrogen applied during paddy irrigation, the peak nitrate nitrogen concentration of 1,620 mg/l is observed at first day due to high permeability and high soil background nitrogen concentration. Additionally, the model results show that the application of high nitrogen content wastewater for irrigation in Ludhiana soil will affect the groundwater quality even when the groundwater table is deep as compared with Kancheepuram soil. © 2015, Indian Academy of Sciences.