Groundwater resources are increasingly exposed to significant overexploitation in many parts of the world, markedly in Iran, one of the most arid areas. The objective of the present study is to investigate the changes in groundwater levels and quality in the Arak aquifer. Groundwater fluctuation contour line maps provided in Geographic Information System (GIS) during 2006 to 2017 in this area indicate that excessive extraction of wells has led to major decline in water levels and a marked increase in concentration of total dissolved solids (TDS). The Groundwater Modeling System (GMS)—a three-dimensional MODFLOW model—paired with MT3D, was utilized to survey the aquifer characterization in the area. In the first step, the conceptual model was developed, and the calibration in both steady and transient states showed that the error between calculated and observed levels was in optimal level. Subsequently, two scenarios were considered to simulate quantity changes in the aquifer: simulation in drought and rainfall reduction and simulation with a 30% increase in well extraction. The results indicate that during both the drought period and increasing exploiting from the pumping wells, the level of water has fallen by more than 5 m. Finally, the calculated hydraulic heads and velocity of flow of ground water in the aquifer are retrieved in the mass transport modeling package MT3D to find the concentration of TDS in the groundwater. Simulation results indicate that concentration of TDS is with far more amount in the areas around the lake located in central parts due to evaporation of Meighan wetland and geological structure of the region. Scenarios considered for prediction by transport model indicate that concentration of TDS would increase if the current situation continues; however, this is mainly influenced by hydrology and geology of the area.