In this study, the HYDRUS-2D/3D was used to simulate nitrate distribution within the soil under surface drip irrigation (DI) and subsurface drip irrigation (SDI) with emitter at depths 10 and 20 cm for tomato crop. Three different soil types (sand, loamy sand, and sandy loam) were considered. Also, the influence of initial soil moisture content on nitrate distribution, leaching out from simulation domain, and uptake by plant roots were investigated. Results showed that the highest percentage of nitrate leaching out from the simulation domain was occurred in sandy soil under the SDI with emitter at depth 20 cm as compared to other irrigation systems. It was about 5% under SDI with 20 cm emitter depth while approximately no leaching was occurred under other irrigation systems. The SDI with shallow emitter depth had the lowest percentage of nitrate leaching out from the simulation domain and the highest nitrate uptake by plant roots. As nitrate is effectively taken up by the plant roots, this will lead to reducing the groundwater contamination risk. Results also showed higher initial soil moisture content leads to augment in the percentage of nitrate leaching out from the simulation domain. Therefore, monitoring of the initial soil moisture content can lead to a good estimation of the nitrate leached to deeper soil layers and the potential of groundwater contamination risk.