Background Nitrate is among major anions in drinking water. Therefore, it is crucial to investigate its concentration in water resources. Modeling is a management strategy to predict the behavior of nitrate in water resources. Objective The current study aimed to predict nitrate concentration in the aquifer of Qazvin plain, using Groundwater Modeling System (GMS). Methods The GMS7.1 software was used to prepare the groundwater flow model. MODFLOW pattern was used to investigate the three-dimensional flow. MT3D pattern was used to assess the changes nitrate concentration in the aquifer. Additionally, several scenarios were designed to evaluate the process of nitrate changes in the aquifer by altering in the aquifer feed and nitrate input rates. Findings There was no anomaly concentration in the aquifer. The scenarios of rainfall reduction suggested that nitrate feed was ineffective in changing nitrate concentration in the aquifer. Moreover, with entry 100, 200, and 300 mg/L of nitrate into the aquifer, the average of nitrate concentration after the end of the two-year periods would increase to 31, 55, and 100mg/L, respectively. Conclusion The obtained results indicated that in a wide area of the saturated aquifer nitrate concentration was below than national standards. Furthermore, high nitrate concentrations were due to the penetrating of the sewage into the aquifer. The outputs of the GMS model suggestd that these conditions could lead to more contamination in central parts of the aquifer.