The goal of this study was to develop a groundwater flow model and a contaminant transport model to understand the fate of the Arsenic in the groundwater. Visual MODFLOW 4.0, the Waterloo Hydrogeologic Inc. software was utilized for this study. A three-dimensional, finite- difference, groundwater flow model was used to develop a regional conceptualization of the flow system in the D. I. Khan area. The D. I. Khan sand aquifer system has been divided into three gently sloping geohydrologic units. The 2900 Km 2 study area was divided into 33852 cells with dimensions of 500 m by 500 m comprising of 186 columns and 182 rows and containing three layers. The finite difference block centered grid was used with an average depth of model simulation was set to 100 meters that almost equals to the average depth of existing tube wells (water wells). The model region was bounded by Indus River, Takwarrah Nala and the Sheikh Haider Zaman Nala in the east, northeast and southwest respectively. The area also consists of Gomal Nala, Chashma Right Bank Canal (CRBC) and Paharpur canal. The model was also adorned with the various hydraulic parameters spatial distributions including hydraulic conductivity (K), initial heads, recharge, porosity, specific storage (Ss), specific yield (Sy), top and bottom elevation of aquifers. The model was initially run for 10 years in steady state for the year 1985. In steady state a single time step was used. The model was calibrated with several runs by modifying the hydraulic conductivities and recharge values. The Parameter Estimation and Testing (PEST) has been used to do the calibration with the minimum and maximum ranges of 30 hydraulic conductivities and recharge values. The model was also calibrated in transient state in 1985 using steady state heads as initial conditions and assessing the draw downs. The area has been studied with respect to the various anthropogenic activities and found to be contaminated with high salinity, sulphates and Arsenic. The contaminant transport model MT3D was used with the observed Arsenic (As) concentrations and calibrated in 2010 for steady state and non steady state conditions. Model realizations were further projected up to 2025 to monitor the spreading of Arsenic concentration in the groundwater. The preliminary management scenarios were also discussed to address the issue at hand for safety of the inhabitants in the study area. The study results include estimates of hydraulic and transport properties, direction of regional flow, contaminant transport, its fate, prevention, remediation and a discussion of the iresults to gain a more complete understanding of the subsurface flow and contaminant transport system. Perhaps this work will be the first step in learning more about the subsurface flow system of the D. I. Khan aquifer, and provide a useful tool to manage and properly plan future management of the groundwater resources.