Today, freight volumes on roads have gone up to a level that there is a need for alternative transport modes. Short Sea Shipping (SSS) is one alternative with a potential that can help reduce the high traffic on roads. Most SSS systems use vessels whereby cargo is rolled on and off using a ramp with very small capacities usually less than 500 TEU, but with increasing cargo traffic, it is not clear if such solutions will be efficient. For ports involved in SSS to meet up this new wave of change, the challenge to make appropriate investments and analysis tools is important. The type of vessel suitable for a SSS operation (such as roll-on roll-off (RoRo), lift-on lift-off (LoLo) etc) has been addressed in this thesis based on their compatibility and cost effectiveness with the terminal equipments. The purpose of this study is to develop an optimization model that can be incorporated into a Computer Decision Support System (DSS) for selecting equipments including ships at a strategic level for investments in handling unitised cargo at port terminals in the context of Short Sea Shipping (SSS). The main contribution of the thesis is the application of computer science techniques in the domain of strategic decision making related to the configuration of complex systems (e.g. interrelationships between ships and equipments) with choices of handling equipment. From modelling the selection of port terminal equipments for SSS, we realised that while integer linear programming is a promising approach for studying such systems, it remains a challenge to handle complex issues in depth especially in relation to the quay crane due to interdependencies between time, cost and capacity of equipments. Model results indicates that a LoLo vessel with a capacity between (500 and 1000 TEU) capable of completing a SSS voyage such that handling is done within 48 hours will be less costly than a RoRo that does it with multiple voyages or one voyage each for multiple RoRo vessels for TEU volumes greater than 1000. But RoRo vessels remain useful for trailers that cannot be transported by LoLo vessels. containers.