The paper describes the methods for the design of systems for implementing intelligent control of transshipping processes at the seaport. Movement of cargo flows requires a constant solution of singular case transportation problems of operational planning and management. The paper shows how the obtained mathematical models of management of cargo flow movement processes, allow for solving optimization problems of the divergent options of bulk cargo movement within the Functioning of infrastructures within a seaport, as well as their communication with suppliers and consumers of loads within the transshipping complex. Modeling of different options bulk cargo movement is needed for providing the given intensity of ship loading taking into account various factors, including weather. The designed model allows for solving the scheduling problems the execution of works on cargo handling in the seaport terminals.