The present work contributes to the numerical simulation of complex turbulent multiphasic fluid flows encountered in estuarine channels. A numerical solution is based on Reynolds averaged Navier-Stokes equations using the mass preserving model based on the so-called Raviart-Thomas finite element on the unstructured mesh in the horizontal plane. In the vertical, the computational domain is divided into number of layers at predefined heights and the method uses a conventional conforming finite element scheme, with the advantage that the lowermost and uppermost layers variable height allow a faithful representation of the time-varying bed and free surface, respectively. A robust up-to-date algorithm is used for computing the eddy viscosity from the efficient
turbulence model for variable density fluid flows. Finally, the capability and the predicting performance of the model are successfully evaluated by applying it to the simulation of the Po River Estuary (PRE) in Italy.