Due to the growing population, crop production is one of the essential needs of the society. Since soil and water salinity can have a great impact on the crop yield loss; so, the appropriate irrigation method can be applied to reduce these effects. In this study, the system dynamics model was developed using VENSIM. The model simulated the effect of salinity and water stress on the crop yield, moisture and salinity of the root zone. In order to calibrate and validate the model results, 9 treatments data were collected from the Right Abshar Irrigation Network, on the Zayandehrud basin. After statistical analysis and calculation of RMSE index and the standard error, the fit between the measured and simulated crop yield, the moisture and salinity of root zone was calculated. The average of these indexes for all treatments was 2776.98 kg/ha and 0.07 for crop yield, 0.026 and 0.09 for soil moisture and final, 0.54 dS/m and 0.08 for the salinity of root zone, respectively. The results showed that the model could be calibrated accurately and completely in estimating the crop yield with the reasonable accuracy.