Rivers have an important role to play in providing most of the water needed for agriculture, industry and domestic consumptions. They also are amongst the important economic and social arteries of various human societies rooted in the lives of people in every land. Most of surface water contaminations are non-point source pollutants which generally contain various forms of nitrogen and phosphorus. In this study, the amount of nitrate input from agricultural lands to Zanjanrood River has been simulated using the SWAT model. In order to calibrate and validate the results, SWAT-CUP software and measured mean monthly average flow rate at Sarcham hydrometric station (1996-2013) were used and 26 sensitive parameters were selected for sensitivity analysis. Three scenarios for irrigation practices, three scenarios for fertilizer rates and two integrated scenarios were defined. The p-factor and r-factor indices were used for uncertainty analysis and two statistical indices, i.e. determination coefficient (R2) and Nash-Sutcliff (NS) coefficient, were used for quality analysis of the results, . In the monthly runoff calibration, at the basin outlet, the coefficients r-factor, p-factor, R2, and NS were 0.27, 0.11, 0.83, and 0.53, respectively. At the validation stage, they were respectively estimated as 0.6, 0.18, 0.73 and 0.53. The results showed that by increasing the pressurized irrigation, the nitrate pollution in the basin was not significantly affected. With regard to fertilizer levels, by reducing consumption of urea fertilizers up to 50%, the amount of nitrate input into the Zanjanrood River reduced by up to about 16.7%. On the other hand, an increase of 50% in fertilizer use has increased nitrate input into the river by 17.2%. The study suggests that changing the surface irrigation method does not lead to a significant change in the average nitrate output from the basin. Also, reducing the amount of fertilization and preventing unnecessary fertilizations by farmers, can greatly prevent the pollution of water resources.