A numerical model for simulations of non-hydrostatic free-surface flows in coastal and estuarine environment, which takes into consideration the impact of suspended matter on flow dynamics through changes in the average density of a suspension, is presented. In contrast to the majority of models, which use hydrostatic pressure approximation, this model considers pressure as non-hydrostatic and solves the dynamic equation for vertical velocity component. An example of the application of the model to the well-known lock-exchange problem has shown that changes in the average medium density caused by particulate suspended matter can induce baro-clinic flows accompanied by the generation of Kelvin-Helmholtz eddies and ripple-kind depositions of particulate matter on the bottom.