Most surface water contaminations are non-point source pollutants, which generally contain various forms of nitrogen and phosphorus. In this study, the amount of nitrate and phosphate leaching from agricultural lands to Zanjanrood River has been simulated using the SWAT model. In order to calibrate and validate the SWAT model, the measured average monthly discharges at Sarcham station were used and the SWAT-CUP model was applied for performing the uncertainty and sensitivity analyses. Three scenarios for irrigation methods and five scenarios for fertilizer rates were defined. The p-factor and r-factor were used for uncertainty analysis and two statistical indices of determination coefficient (R2) and Nash-Sutcliffe efficiency (NS) were utilized for the validation model. For the calibration of monthly runoff at the basin’s outlet, the coefficients of r-factor, p-factor, R2, NS were obtained as 0.27, 0.11, 0.83, and 0.53, respectively. The results showed with increasing the pressurized irrigation areas, the nitrate and phosphate pollutions in the river basin are not significantly affected. With regard to fertilizer rates, by reducing the consumption of urea and phosphate fertilizers up to 50%, the amount of nitrate and phosphate leaching into the Zanjanrood River reduced up to 16.7% and 19.2%, respectively. On the other hand, an increase of 50% in fertilizer application has increased nitrate and phosphate leaching into the river by 17.2% and 17.7%, respectively. In addition, reducing the fertilization rate and preventing unnecessary fertilization by farmers, water resources pollution can be considerably prevented.