Seaports of the world, which built in estuaries and bays, are connected to the seas by approach channels. When they crossing shallow water depths (milky water and surf zones), they are subjected to intensive drift by bottom sediments. It is main reason of decreasing of the depths in the channels over time and to reduce the terms between repair dredging works. The wave velocities are the main reason force of movement of bottom sediments. Projections of the velocities of water particles in waves on shallow water are described by various wave theories. Intensity of drifting to deposit due to a number of natural factors: topography of the sea beds; duration and the severity of storms; speeds of currents; types of bottom soils and their physical and mechanical characteristics. In addition, this process is influenced by the design profile of the channels and their planned position to the seaport gates. In the process of engineering studies and scientific support for the design of sea channels, the total volume of sediment flows and their general direction of transit are established, options for the planned location of channels routes, the angles of their slopes as well as options for protecting channels from drifting sediment are considered, taking into account the factors listed above. The analysis of all factors, as well as, the results physical and mathematical modeling allows take optimal design decisions on the location of the routes of sea channels, their dimensions taking into account the specifics of regions. The dimensions of estimated vessels, types of channels and cargo turnover of sea ports in the near future are also taken into account. The main requirements that apply to sea channels in their design are safe navigation of ships, the minimum amount of dredging works, as in the construction process, as well as exploitation. For this reason, the protection of sea channels from drifting by sediments is a very urgent technical problem. This problem was solved on the basis of analysis of existing methods for protection of sea channels in the shallow-water zones of the seas from the bottom sediments by developing a simple and inexpensive method. The mechanism of movement of bottom sediments under the action of wind waves and current was taking into account, when developing this method. The method proposed in this article is based on the principal of operation of a flexible floating breakwater, which patented in the state Ukraine.