Port cities and their neighbouring areas, located at the confines between sea and land, are key hubs in the transportation of goods and people. Ports serve global transport needs, while they are embedded in local geographies, topographies, political, economic and historical settlements. People have always been attracted to human settlements at the interface of water and land. These settlements have evolved into large population centres and metropolitan areas. Major cities, economic hubs and trade centres are engines of key importance for expansive territories and the ports in their vicinity, but they are also places at the forefront of many contemporary threats, including sea level rise as a consequence of climate change. Today, according to the United Nations Development Programme, 55% of humans worldwide live in cities and 40% live within 100 kms off the coast, thus in the vicinity of water-related threats. Maritime and logistic flows cross ports and densely built territories, creating additional environmental and other challenges. The war in Ukraine, long periods of drought and excessive water levels due to heavy rainfall in Pakistan are only the latest examples of both the need for and the danger of port activities for cities and landscapes. Nonetheless, a comprehensive understanding of the relationships between ports, cities and their territories is missing. This special issue argues that we need to embrace a holistic, inclusive approach to port city development, based on ecosystems values, embedded in various layers of capital: natural, cultural, social, human, industrial and creative. To achieve a port city symbiosis and avoid parasitism—defined here as a relationship where one partner benefits at the expense of another-, new port governance frameworks will have to answer to what knowledge needs to be shared to make multiple value creation in the port city ecosystem happen. For transitions to happen, port city territories will have to nurture ecosystem values to unlock this capital. New governance constellations will have to be based on shared mindsets, deeper understanding of the interests of local communities, and a set of collaborative principles. What exactly the relationships are between port, city and territory, how maritime flows relate to them, and whether or to what degree these connections are symbiotic or parasitic is subject for further exploration. Exploring the concept of symbiosis in port city ecosystems is fundamental for human activities, including economic ones, to sustain themselves in healthy, clean, green, liveable port cities and coastal communities. In this introduction we reflect on contributions by authors who examine port city symbiosis in various seaports in the Netherlands, Chile, United States, Portugal, as well as inland ports in France, Belgium, Switzerland and Germany.