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Cities and urbanized regions are complex, dynamic, and highly integrated systems linking social, ecological, and technical infrastructure domains in ways that create deep challenges for good governance, policymaking, and planning. The combination of impacts from climate change in cities, air pollution, rapid population growth, multiple sources of development pressure and overall urban system complexity make it difficult for decision-makers to develop and guide development trajectories along more livable, equitable, and at the same time, more resilient pathways. Advancing urban sustainability and resilience agendas requires expanding the scope of inter- and trans-disciplinarity approaches, moving beyond the historically separate social–ecological and socio-technical approaches to jointly study social–ecological–technical infrastructure systems in cities. We take urban complexity as a given and suggest that in both research and practice we need to better capture and understand feedbacks, interdependencies, and non-linearities which create uncertainties and challenge the efficacy of governance practices to achieve normative goals for society. Here, we explore new methods, tools, and approaches to advance our understanding of urban system complexity through a series of journal special issue articles that examine urban structure–function relationships, urban sustainability transitions, green space availability, social–ecological memory, functional traits, and urban land use scenarios. [ABSTRACT FROM AUTHOR]