Abstarct: Agricultural activities are the most significant anthropogenic sources of nitrate pollution in ground water and nitrate leaching from this systems has direct impact on ground water quality. The importance of ground water pollution, due to extravagance in application of N fertilizers in intensive agricultural areas has been increased during last decade. We have to know that increasing of the yield shouldn t make to destroyed the environment. Increasing of production in unit area and improving of yield quantity and quality need special notation. Changing of irrigation systems from current methods such as surface irrigation to advance systems such as drip irrigation can be has important role in this case, because application of this systems cause increasing of water use efficiency. Fertigation is the most effective water application method in vegetables and garden crops, which is working with drip irrigation system. In order to more survey this system s efficiency perform an experiment contacted with 4 treatments with transplanting of tomato crop in Bastam, Shahrood, which involves 3 treatments with drip irrigation and fourth treatment to surface irrigation. To analyze and obtain more complete information from results I used an advanced model HYDRUS-2D. Results of research indicated that the strategy of weekly fertigation and alternate day irrigation is increasing water and nitrogen use efficiency. Another result showed that average yield of drip irrigation was 72.56 t/ha which is showing increasing of 30 percent yield with compare to surface irrigation and also it is showing 116 percent more yield with compare to yield of tomato in Bastam area. Also results of simulation of water and nitrate movement in soil laxyers showed that water and nutrient distribution during plant growth period were proportionate with root development depth and so were available in the plant requirement time, that is demonstrated high efficiency of fertigation system. Another results of modeling study is real estimating of drainage water and nitrate leaching below crop root zone in the plant growth season. Numerical analysis of model results showed that drainage water below root zone was only 0.3 percent of applied water and leaching of nitrate below this zone was 3.29 percent of total useable nitrate which indicate that high percent of water and nutrient were concentrated in root extension zone.