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Application of natural products that would improve fertilizer use efficiency and at the same time reduce nitrate leaching is of great interest. Zeolites are a group of natural minerals that due to their high cation exchange capacity are potentially suitable soil amendments and/or carriers of plant nutrients. In this study, the effect of clinoptilolite zeolite, as a soil amendment, on the parameters related to water and nitrogen movement in soil was investigated. Parameter and uncertainty estimation in the unamended (control) and amended soil (Z) was performed using the sequential uncertainty fitting algorithm (SUFI-2) which is linked to LEACHN (in the LEACHN-CUP software). P-factor, R-factor (which show goodness of prediction uncertainty), and Nash-Sutcliffe coefficient (NS) obtained 0.71, 0.76, and 0.92, respectively, in the prediction of accumulated drainage from control. The results in prediction of the accumulated drainage from Z treatment using hydraulic parameters obtained in control was satisfactory (P-factor = 0.87, R-factor = 0.78, and NS = 0.87). P-factor, R- factor, and NS were 0.87, 1.36, and 0.91, respectively, in the prediction of NO3-N leaching at control.According to the P-factor and R-factor values (P-factor = 1, R-factor = 2.46), application of thecontrol parameter ranges in the prediction of NO3-N leaching at Z treatment produced a large uncertainty. By adjusting the parameters in control for zeolite-amended soil, the estimated values for denitrification rate, distribution coefficient, and soil/solution NO3-N nitrification rate were greater in zeolite-amended soil compared to control.