We present in this paper a study of the main mechanisms of the model groundwater flow and transport model of pollutants in aquifers. The processes associated with the transport of pollutants are studied in detail: diffusion, dispersion and retention of contaminants in the aquifer porous matrix. Is then developed with the support of Visual MODFLOW software v.2011.1, two numerical simulations with synthetic data transport and remediation of a pollutant in the saturated zone of an aquifer composed of three layers. The primary goal of numerical simulation of the groundwater flow model and transport of pollutants studied model is to evaluate the theoretical models and provide a methodological guide computer simulations of the dynamics of ground water and the evolution of pollutant plumes sometidas external condiciones; for example: pumping wells, injection wells, infiltration, etc.. The data used in the simulation represents a synthetic aquifer consists of three layers with a fault in the middle of the system, which allows for hydraulically connecting the surface layer represented by a water aquifer, with the layer represented by a confined aquifer. The second goal is to numerically simulate the process of remediation of polluted aquifers, in order to establish the effectiveness of the method. Particularly was chosen remediation method Pump-and-Treat, treatment of the aquifer most systems used for this purpose, which consists of pumping to the surface of the polluted groundwater for further treatment to remove external contaminants.