While shipping and logistics studies often describe the flows and networks on the level of firms and terminals rather than cities, urban studies pay limited attention to transport infrastructure and material flows. The renewal of network analysis based on complex systems will be discussed in this paper as a potential bridge between those two approaches. It particularly focuses on how transport and urban elements can be mutually integrated. The main conclusion points at the efforts to better untangle network/carrier and urban/territorial effects in the design and operation of shipping and logistics systems.