International trade plays a critical role for the global economy. A significant portion of general consumption goods is transported by vessels in a containerized form. Increasing volumes of the containerized trade impose additional pressure on marine container terminals (MCTs), which are responsible for service of incoming vessels from different liner shipping companies. MCTs are considered as important nodes in supply chains, as they allow transfer of containers from vessels to one of the alternative inland modes (generally, truck or rail). Managing operations within MCTs is a quite challenging task not only due to increasing seaborne trade volumes, but also due to increasing number of liner shipping alliances, deployment of megaships by liner shipping companies, inability to expand the terminal size due to spatial constraints, and other factors. Another important goal for the MCT operator is to ensure the timely service of vessels, as the vessel service delays may result in potential disruption of liner shipping schedules, and ultimately cause product delivery delays to the final customers.This dissertation focuses on addressing complex decision problems, which are faced by the MCT operators. The seaside operations, which deal with loading and unloading of vessels, will be of a primary interest, as they affect the total turnaround time of vessels. The latter is considered as one of the key performance indicators for the MCT operations. As many of decision problems related to the seaside operations, cannot be solved using the exact optimization algorithms (e.g., Simplex, Branch-and-Bound, Brach-and-Cut) within a reasonable computational time for the realistic size problem instances, a number of metaheuristic algorithms will be proposed (with a primary focus on Evolutionary Algorithms, which have been widely used in different fields for solving combinatorial decision problems). The proposed metaheuristic algorithms are expected to serve as efficient decision making tools for the MCT operators and facilitate exchange of freight flows between water and inland transportation modes.