Nitrogen fertilizer is one of the widely used fertilizers, and the nitrogen found in the soil may convert to nitrate and causes soil contamination. In this study, the distribution and uniformity of nitrate in soil in two surface and subsurface drip irrigation systems were compared in a physical model consisting of transparent glass with dimensions of 1.20 * 0.5 * 1 m and the sandy loam soil texture with considering two emitter installation depths of 0 and 30 cm, three flow discharges of Q1=2, Q2=4, Q3=8 L/h and three fertilizer levels of S1=125, S2=250, S3=375 mg/lit. Irrigation was done during six hours and nitrate and moisture sampling were performed 68 hours after the water front advance. The results showed that with increasing flow discharge by two and four times, the wet area is respectively increased by three and five times in the subsurface drip irrigation system. However, in the surface drip irrigation system, the changes in flow discharge and the wet area are approximately the same. Due to this problem, in the subsurface drip irrigation system, with increasing the fertilizer level, the nitrate has extensively spread out and therefore its concentration is reduced. In addition, in the subsurface drip irrigation system, the nitrate concentration increases with increasing the fertilizer level in a given flow discharge and a constant wetted area. On the other hand, in the surface drip irrigation system, the nitrate concentration increases for Q1=2 L/h and decreases for Q2=4 L/h and Q3=8 L/h. By comparing these two systems, it can be concluded that by increasing the flow discharge, nitrate concentration difference increases because of increasing non-uniformity of nitrate distribution in the surface drip irrigation. So that, by increasing the fertilizer concentration, the difference of nitrate concentration between these two methods increases from 22% to 500%, 43 % to 352% and 14% to 166%, respectively. So, it can be said that the subsurface drip irrigation system