Globalization and containerization have significantly increased the volume of shipping in international trade. A seaport is a critical component in maritime transportation. Currently, the main focus for the effective functioning of commercial ports is focused on the use of the latest information technologies. Information support of the port operation is a difficult task for a variety of reasons, the main of which is the external influence on the internal operations of the port and its overall efficiency. Simulation modeling is the most suitable tool for analyzing such a complex interaction. The article defines the characteristic features describing the specifics of the seaport operation in the AnyLogic simulation program. Various possibilities of using the established simulation model are shown to determine the limitations in the size of the throughput and processing capacity of the seaport, substantiate the need to create a “dry” port and select its main parameters.