Selecting the best scenario of intervention to improve the functioning of complex systems represents a troublesome task both for public and private decision makers, since it requires the deployment of appropriate analysis and evaluation tools. In the case of intermodal transport systems, complexity is given by the execution of different types of activities using various resources, and by the presence of several actors operating in the same environment with diverse goals. In this paper, an integrated approach to assess design alternatives regarding rail port operations is proposed by combining business process modeling and multi-actor multi-criteria evaluation. In fact, a railway process has been graphically represented by means of the standardized modeling language called Business Process Modeling and Notation (BPMN) at different levels of detail, i.e. taking into account not only the actual transport operations but also the necessary documentary procedures to perform the freight transfer services. In addition to the identification of possible bottlenecks, the analysis of the considered railway process has enabled the determination of its most significant features. These parameters have been subsequently used as some of the criteria according to which the performances of the examined scenarios of intervention have been evaluated, adopting the Analytic Hierarchy Process (AHP) technique. Furthermore, the appraisal has been enhanced by explicitly including the key stakeholders involved in the railway process at hand. The developed methodology has been applied to the case study of the Port of Trieste, Italy, in order to investigate possibilities for an increase in railway capacity.