The data completion method combined with the modeling of water flow and solute transport in saturated porous media is used twice to identify the extent of polluted water intrusion from the downstream boundary of an aquifer. The aim of this work is to solve the problem even though data are missing on some of the boundaries, by exploiting the fact that there are over specified data on the other boundaries. Indeed, it is assumed that the flow and the water head are known on the upstream boundary while the pollutant concentrations are known on the downstream boundary. The method developed in this work allows to determine the flows, water heads and pollutant concentrations in the whole domain. The method is applied in different aquifer configurations with pumping wells, the results are satisfactory. The model developed has shown its effectiveness in detecting the intrusion of polluted water and can be used in real cases.