The statistical techniques based on compositional data are applied to investigate the evolution of the traffic share of the container throughput in a multi-port system. Compositional vectors are those which contain relative information of parts of some whole. The application of conventional statistical techniques to compositional data may lead to erroneous conclusions and spurious correlations. Therefore, compositional data (CoDa) should be treated taking into account their own mathematical structure. The so-called log-ratio approach provides a set of transformations that allow to apply conventional statistical techniques to the transformed compositional data samples. Thus, the objective of this paper is double. As a first stage it aims to introduce the CoDa formalism and highlight its potentiality in the port container throughput analysis as example of transport system providing an applied example: the container throughput evolution in the Spanish Mediterranean Ports system during the period 1976–2015. Second, based on the previous analysis, the aim is to characterize the container throughput in SpanishMed ports and its temporal evolution. The CoDa analysis clarifies the interpretation and data association of the container traffic throughput evolution in function of some selected change points: boom of containerization in 1990s and 2008 crisis. This contribution proves that the CoDa methodology is useful to investigate the complexity of the transport disciplines in order to understand and to manage the spatial integration that results from the movement of people and freight.