This paper presents numerical analysis of nitrate contamination transport through soils. Two cases of drain, a trapezoidal canal and a well were considered in the analysis. Modelling of contaminant transport is carried out using GeoStudio programme. Particle tracking analysis established the flow paths of contaminant migration from source to drain. Advection–dispersion analysis showed contours of nitrate concentration in the subsurface with time. To control the contaminant transport, impervious vertical barriers of different depths were inserted at different locations in the numerical model. Results demonstrated that the nitrate concentration after 100 days decreased by about 40% with the inclusion of a vertical barrier of 6 m deep on the source side, whereas it reduced by about 95% when the depth of the barrier was increased to 10 m. For a trapezoidal canal drain, when the vertical barrier is placed on the drain side, the reduction in nitrate concentration was much lesser, indicating that the vertical barriers are more effective when they are placed on the source side. Effect of the depth of contaminant source with respect to the drain is studied though numerical simulations. Further, the nitrate concentration is analyzed with a well drain for 500 days for two different source depths of 2 and 2.5 m. Results showed that the nitrate concentration decreased with the increase in distance from the source. However, there was no significant change in the concentration at all locations, beyond 40 days, suggesting that the pollutant concentration has reached an equilibrium condition in 40 days.