This study considers the Dynamic Minimum Cost Hybrid Berth Allocation Problem (DMCHBAP) with fixed handling times of vessels. The objective function to be minimized consists of three components: costs of positioning, waiting, and tardiness of completion for all vessels. A mathematical formulation of DMCHBAP, based on Mixed Integer Linear Programming (MILP), is proposed and used within the framework of commercial CPLEX 12.3 solver. As the speed of finding high-quality solutions is of crucial importance for an efficient and reliable decision support system in container terminal, two population-based metaheuristic approaches to DMCHBAP are proposed: combined Genetic Algorithm (cGA) and improvement-based Bee Colony Optimization (BCOi). Both cGA and BCOi are evaluated and compared against each other and against state-of-the-art solution methods for DMCHBAP on five sets of problem instances. The conducted computational experiments and statistical analysis indicate that population-based metaheuristic methods represent promising approaches for DMCHBAP and similar problems in maritime transportation.