This paper focuses on the operational and strategic planning decisions related to the quayside of container terminals. We introduce an integrated operational research (OR) and system dynamics (SD) approach to solve the Berth Allocation Problem (BAP) and the Quay Crane Assignment Problem (QCAP). A BAPQCAP optimization modeling approach which considers practical aspects not studied before in the integration of BAP and QCAP is discussed. A conceptual SD model is developed to determine the long-term effect of optimization on the system behavior factors like resource utilization, attractiveness to port, number of incoming vessels to port and port profits. The framework can be used for improving the operational efficiency of container terminals and providing a strategic view after applying optimization.