The Indonesian fertiliser industry is a significant contributor to the national economy. Given the need to distribute its products to customers on the 17,000 islands making up availability of ports are major factors in managing fertiliser product lifecycles. However, managing the flow of material around a port is a complex process, affected by a range of socio-technical factors. This paper proposes a conceptual model of supply network processes and their relationships to infrastructures such as ports based on a socio-technical systems analysis of material flow. Results from an application of the model to explore how changes to a port is operated affect material flow. These results were used to inform the development of an agent based simulation model to support decision makers in investigating the effects of their decisions in considering the impact of potential management interventions on the flow of materials within the port. The conceptual and simulation models are illustrated using a case study taken from a port in the Indonesian fertiliser industry.