The size of container ships is constantly growing over recent decades due to a continuous search for economies of scale by shipping lines. The growth of the container ships has necessitated ports to adapt, e.g. by increasing the water depth requirements. Many of the conventional onshore ports cannot receive larger ships without dredging activities due to depth restrictions. A considerable amount of dredging is necessary to create an access channel to reach deep waters. The development of offshore-onshore port systems can be a huge opportunity for coastal zones with an extensive shallow foreshore to limit the channel dredging costs. However, the methodology for evaluating the design of innovative solutions, like offshore-onshore port systems, is limited compared to the evaluation of conventional onshore port designs. A framework, including the cost-based evaluations, could serve as a reference to make more deliberate and integral choices between various types of port systems. Therefore, the objective of this research is to evaluate the major logistical trade-offs regarding various types of port systems based on costs. Three port system alternatives, including the associated characteristics, are introduced: i) an onshore port system, ii) an offshore-onshore port system with a waterway transport link and iii) an offshore-onshore port system with a fixed infrastructure link. Next, two characteristic design variables are identified to specify the design scenarios: i) the capacity of the design vessel and ii) the distance between the offshore and onshore terminal. The developed model comprises two parts. The first part is developed to determine the required port system elements and to make the corresponding cost estimates for the specified design scenarios, for all three port system alternatives. The second part is developed to address the logistics of the offshore-onshore port system with a waterway transport link. The results show that the cost estimates of offshore-onshore port systems can be less costly compared to the cost estimates for the onshore port system for specific design scenarios. Hence both offshore-onshore port systems offer less costly alternatives compared to the onshore port system for specific design scenarios. From this, we can conclude that offshore-onshore port systems will be considered more frequently in the future, as the size of container ships is still growing. The framework - a collection of concepts - results in a better understanding of the logistical trade-offs between different type of port systems for container transport and handling. The major logistical trade-offs are framed based on the evaluation of the characteristic design variables, the results of the sensitivity analyses and the assessment of the relationship between the operational reliability of the waterway transport link and the required storage capacities. The logistical simulation is the first method to relate the container ship and shuttle barge transport with the terminal operations using agent-based discrete-event simulations. These logistical simulations evaluate the cost related to the shuttle barge downtime. Depending on the frequency and length of the periods of downtime, the most cost-effective solutions are found for specific downtime scenarios.