Groundwater pollution is one of the most important challenges for human. In many parts of the world, groundwater is used for agriculture and even drinking, whereas natural and human-made groundwater contaminants have also affected the quality of these waters. Therefore, monitoring and evaluating the quantity and quality of groundwater is very important. In this research, the efficiency of finite element method (FEM) for groundwater flow and Sulfate concentration transport modeling has been investigated for a 7-year period. After finite element validation analysis, this method was employed in a hypothetical and real-case aquifer with regularly distributed nodes and square elements 200 m × 200 m. The mean error and root mean square error (RMSE) as performance criteria were used to evaluate the performance of the model. The results indicated that the FEM model with RMSE = 1.06 (m) and 1.44 (me/lit) has good skills in groundwater flow and contaminant transport modeling, respectively. Also, the results of the FEM model indicated that in the northeast of the aquifer, the groundwater level is low and the amount of Sulfate is high (higher than the standard values recommended by) which is also confirmed by real data.