Groundwater resources are increasingly exposed to significant overexploitation in many parts of the world, markedly in Iran, one of the most arid areas. Social, economic and environmental aspects including water quality and quantity concerns are necessary for sustainable management of water resources. The aim of the current study was to investigate the changes in groundwater levels and quality in the Isfahan-Borkhar aquifer. Groundwater fluctuation contour lines maps provided in Geographic Information System (GIS) during 1971-2005 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, a three-dimensional MODFLOW model paired with MT3D, was utilized to survey the aquifer characterization in the area. In the first step, usage high amount of hydrological and geological data, the conceptual model was developed and calibrated in both steady and transient states. The results of the calibration showed that the error between calculated and observed levels was in optimal level. Subsequently, since rainfall is decreasing annually in the study area and the aquifer is in danger of drought, and uncontrolled exploitation of wells has led it to a crisis, two scenarios were considered to simulate quantity changes in the aquifer: Simulation in drought and rainfall reduction. The results indicate that during both the drought period and increasing exploiting from the pumping wells, the level of water has fallen 0.5-0.1 m/s annually, and it will destroy the aquifer. Finally, the calculated hydraulic heads and velocity of flow of groundwater in the aquifer are recovered in the mass transport modelling 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 Borkhar-Isfahan Aquifer and geological structure of the region. Scenarios considered for prediction by transport model show that concentration of TDS would enhance if the current situation continues; however, this is mainly influenced by hydrology and geology of the area.