The hydraulics theory and wind-wave modelling are used to model annual changes of a threshold (sand bar) height at the mouth of the Narva River in 2002. The changes in the threshold height are attributed to two mechanisms: the cross-shore sediment transport driven by the river flow that erodes the obstacle and the long-shore transport forced by waves that increases the threshold height. It is shown that the flow stratification in the river mouth switches between one- and two-layer modes in different seasons, depending on variations of water level, river discharge and wave activity.