When planning to change operations at ports there are two key stake holders with very different interests involved in the decision making processes. Port operators are attentive to their standards, a smooth service flow and economic viability while border agencies are concerned about national security. The time taken for security checks often interferes with the compliance to service standards that port operators would like to achieve. Decision support tools as for example Cost-Benefit Analysis or Multi Criteria Analysis are useful helpers to better understand the impact of changes to a system. They allow investigating future scenarios and helping to find solutions that are acceptable for all parties involved in port operations. In this paper we evaluate two different modelling methods, namely scenario analysis and discrete event simulation. These are useful for driving the decision support tools (i.e. they provide the inputs the decision support tools require). Our aims are, on the one hand, to guide the reader through the modelling processes and, on the other hand, to demonstrate what kind of decision support information one can obtain from the different modelling methods presented.