Arsenic contaminated shallow aquifers evaluation, mitigation, and management strategies are the challenging task to all the hydrologist and provide a safe drinking water demand in the Holocene age, alluvial aquifers. To manage and mitigate such problems, we used numerical groundwater modeling software (GMS 10.2), for the development of 3D transient state predictive (groundwater flow and contaminant transport) conceptual model for two topographically different arsenic contaminated regions. The models were built by using the measured hydro-geological data, empirical values, and equations. Groundwater flow calibration, sensitivity analyses, and validation were performed for each soil parameters, varying boundary conditions and for alternate meteorological scenarios. The MODFLOW results suggested that, the distribution of As contaminant was directly controlled by the complex hydrostratigraphy, surface water bodies and indirectly controlled by the change in meteorological conditions. The MT3DMS model, for As contaminant transport, used for the assessment of shallow and deeper aquifers. The results showed that the downward movement of As has made the deeper aquifer unsafe for drinking water and irrigation purposes. However, the aquifers and regions with high flushing capability, negligible vertical hydraulic conductivity can be delineated as As safe groundwater source, irrespective of their sediment color. Therefore, for the geogenic source of As, both the simulation results inferred that to estimate and mitigate As contaminant groundwater aquifers or regions, the numerical modeling solution is a technically viable means an effective decision-making tool.