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Indonesia, a large archipelago with more than 17,500 islands, about 5000 km across, is crucially dependent on maritime transport for connectivity. Freight transport is associated with high logistic costs. It has been estimated that logistic costs amount to 26% of gross domestic product. National economic growth and competitiveness will critically depend on strategic choices for the further development of large maritime networks. The objective of this chapter is to present the recent modeling work undertaken to support these policies. The modeling centered around the optimization of the maritime network of Indonesia. It required the development of a full maritime freight demand and supply model system. The Indonesian maritime freight transport system was analyzed in two main segments in different studies. First, we considered the subsidized, combined passenger/cargo ferry services (Perintis), which provide basic …