The cyber-physical nature of engineering systems requires the smooth integration of decision making across soft and hard infrastructure. This need is common to any systems where decision making considers multiple complex systems such as the climate, the natural and built environment, and the dynamics of large organisations. As an example, in the Anthropocene, acute droughts and floods cannot only be imputed to more extreme variations of the climate patterns, but also to the alteration of the habitable environment and of the resources that support it, hence to their governance and management. In this discussion paper we present arguments about the extent to which the natural environment is modified to support urbanisation. We expose the cyber-physical nature of large infrastructure systems taking as an exam-ple the events of the 2011 Brisbane flood and the operations of the damming system of the river Brisbane. Using literature resources and data, we show how flood defence devices had to provide for a population of almost 2 million people, while being engineered when the population was less than one million, with increase in water withdrawal mainly due to resi-dential utilities. We show how the cyber-physical aspects of the problem materialised in moth-long delays in the gover-nance and management structure and made the flood event transcend the boundary of a purely climatic or engineering incident. Looking beyond the Brisbane example, our conclusions point at overcoming the discontinuity between opera-tion, management and political layers when operating on cyber-physical systems such as freshwater networks.