Prescriptions for a more sustainable society are usually piecemeal. They are inspired by single issue criteria, no matter if sustainability is, rather, a whole system trait as it pertains to growth and development, that are overall system attributes. In this paper urban sustainability is discussed in a whole system perspective using the ecosystem approach as a framework. This required that urban systems were described as flow networks and investigated through ecological network analysis. Three cities are discussed as a case study and their network representation concerned water flows that were identified knowing water exchanges between city components (i.e. sectors of human activity). Network analysis yielded system level indices that condense the complexity of the flow structure (representing system’s metabolism) in a few measures that provide information on how systems grow and develop; as such they allow to explore sustainability at the whole system scale. For every system the present network is compared with an alternative scenario envisioned considering policies that foster sustainability. The results show that although all the alternative scenarios would improve sustainability through reducing water consumption, effects at the whole system level may diverge from the expectation. Because system sustainability depends on the balance between organization of flows (order and coherence of flows) and flexibility (redundancy of connections), network reshaping may bring about a reduction in both these fundamental properties, with negative effects on system’s propensity to be sustainable. System level indices are holistic measures that unveil the relation between internal processes and whole system performance. Understanding this relation is crucial because the former are the target of environmental policies but sustainability, the objective of such policies, is an overall system trait.