The literature about seaport operations emphasizes the fact that numbers of resources utilized at seaport terminals add multitude of complexities to optimization problems. In such dynamic environments, there has been a need for solving each complex operational problem to increase service efficiency and to improve effectiveness of seaport's IT services and thus seaport's competitiveness. By implementing optimal solutions and putting into practice of heuristic methods, multitude of operational problems can be solved. Computational results reveal that applied methods are efficient, versatile, and easy to use in solving problems. As an outcome, this thesis offers mathematical and process models, high performing optimization algorithms, and optimization solutions for container terminal operations. In addition, the thesis states key seaport logistics problems and propose innovative algorithms for solving complex combinatorial seaport logistics problems. Computational results present that the proposed algorithms are efficient, convenient, and applicable stochastic methods for solving optimization problems of seaport logistics operations. Additionally, because of the wide applicability of seaport operational research solutions, the thesis not only specifically proposes solutions for Izmir seaport, but also presents solutions for wide range of global seaports operations.