The aim of this work is to study the dynamics of bottom sediments granulometric fractions in the Kalamitsky Gulf coastal zone near the Lake Sakskoe bay-bar under influence of storm surge based on the XBeach numerical morphodynamic model. A series of numerical experiments has been carried out, in which the parameters of waves at the seaward boundary of the computational domain changed in time, simulating the passage of a cyclonic atmospheric anomaly over the investigated region. The initial distribution of the sediment volume concentrations in different parts of the underwater coastal slope profile was set based on the results of field observations. The duration of model calculations was 24 h. The quantitative characteristics of the spatial distribution of various bottom sediments fractions, sediments median diameter and values of bottom deformations were obtained. It has been established that the main morphodynamic changes occurs in the area 0–120 m from the shoreline and are limited by the 3.5 m isobath. It was noted that the maximum changes in the relief of the coastal zone and the upper section of the underwater coastal slope occur during the development and attenuation phases of a storm. In the same time intervals an intensive redistribution of sandy material is observed. It has been established that, with a change in the parameters of wind waves in time at the seaward boundary, the scales of sand material redistribution and deformations of the coastal zone are higher than in the experiment when the direction of the waves does not change with time at the seaward boundary of the computational domain.