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Cities are increasingly governed through indicator systems, including sustainability dashboards, SDG monitoring platforms, resilience indices, and performance metrics. These systems do more than describe cities: they shape what becomes visible, governable, and politically actionable. Yet many critical processes shaping urban sustainability and climate resilience remain only partially visible. In particular, flows of energy, materials, goods, people, waste, and information structure how cities function, adapt, and transform, but are often fragmented or weakly represented compared to static indicators of infrastructure, land use, or emissions. This contribution examines how contemporary urban indicator systems conceptualize sustainability and resilience, focusing on what they make visible and what they leave invisible. Based on a comparative review of sustainability, resilience, and climate-monitoring frameworks, we assess how key urban flows are currently represented. The assessment is expected to clarify the extent to which current indicator systems emphasize sectoral performance and fixed structures, relative to their treatment of dynamic interactions, feedbacks, and cross-sectoral dependencies. Building on this diagnosis, the paper proposes design principles for indicator systems that better capture the “invisible city” and support resilient and sustainable urban transitions.