Density gradients can be included in the hydrodynamic simulation if the water mass is well mixed, such that the temperature and salinity and thus the density is almost constant over the depth. The density gradient is counteracted by the water-level gradients and in estuaries density gradients may result in set-up of the water level of several cm. In most cases the effect of the density gradients in 2D shallow water equations is small and hence the density terms can be neglected. If the density variation over the depth is significant you should apply the 3-dimensional flow model.