Container terminals (CTs) play an essential role in the global transportation system. To deal with growing container shipments, a CT needs to better solve the three essential seaside operational problems; berth allocation problem (BAP), quay crane assignment problem (QCAP), and quay crane scheduling problem (QCSP), which affect the performance of a CT considerably. In past studies, the three seaside operational problems have often been solved individually or partially, which is likely to result in poor overall system performance. However, solving the three seaside operational problems simultaneously is in fact a very complicated task. In this research, we dealt with the three seaside operational problems at the same time by using a novel high-level Petri net, termed an Object-Oriented and Timed Predicate/Transition Net (OOTPr/Tr net). After defining the three seaside operational problems formally, we integrated them as a three-level framework that was further transformed into an OOTPr/Tr net model. Then, using the Prolog programming language, we implemented this model as a simulation tool to find the best solution based on the various combinations of heuristic rules used.